Multiple platform build/check report for BioC 3.9 - BUILD BIN report for rTANDEM on celaya2

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### Running command:
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###   rm -rf rTANDEM.buildbin-libdir && mkdir rTANDEM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rTANDEM_1.24.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R rTANDEM.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rTANDEM.buildbin-libdir rTANDEM_1.24.0.tar.gz'
>>>>>>> 

* installing *source* package ‘rTANDEM’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c PTMTreeSearch.cpp -o PTMTreeSearch.o
In file included from PTMTreeSearch.cpp:14:
In file included from ./PTMTreeSearch.h:16:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
In file included from PTMTreeSearch.cpp:16:
In file included from ./mscore.h:146:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pOut;
                ^
                      []
./mmotif.h:295:16: note: allocated with 'new[]' here
                char *pOut = new char[256];
                             ^
PTMTreeSearch.cpp:382:12: warning: unused variable 'dMaxExpect' [-Wunused-variable]
    double dMaxExpect = atof(strValue.c_str());
           ^
PTMTreeSearch.cpp:402:54: warning: array subscript is of type 'char' [-Wchar-subscripts]
          for (unsigned int k = 1; k < m_vmodModificationsDB[itAa->m_cRes].size(); k++){
                                                            ^~~~~~~~~~~~~
PTMTreeSearch.cpp:403:21: warning: array subscript is of type 'char' [-Wchar-subscripts]
            if (floor((mods[itAa->m_cRes][k])*10000) == iModSize){
                           ^~~~~~~~~~~~~
PTMTreeSearch.cpp:405:24: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_vmodModificationsDB[itAa->m_cRes][k].m_uiCount++;
                                     ^~~~~~~~~~~~~
PTMTreeSearch.cpp:406:28: warning: array subscript is of type 'char' [-Wchar-subscripts]
                if (m_vmodModificationsDB[itAa->m_cRes][k].m_dTarget < itAa->m_fPval-1.0)
                                         ^~~~~~~~~~~~~
PTMTreeSearch.cpp:407:26: warning: array subscript is of type 'char' [-Wchar-subscripts]
                  m_vmodModificationsDB[itAa->m_cRes][k].m_dTarget = itAa->m_fPval-1.0;
                                       ^~~~~~~~~~~~~
PTMTreeSearch.cpp:408:28: warning: array subscript is of type 'char' [-Wchar-subscripts]
                if (m_vmodModificationsDB[itAa->m_cRes][k].m_dTargetEval > expect)
                                         ^~~~~~~~~~~~~
PTMTreeSearch.cpp:409:26: warning: array subscript is of type 'char' [-Wchar-subscripts]
                  m_vmodModificationsDB[itAa->m_cRes][k].m_dTargetEval = expect;
                                       ^~~~~~~~~~~~~
PTMTreeSearch.cpp:380:10: warning: unused variable 'dMaxExpect' [-Wunused-variable]
  double dMaxExpect = 0.1;
         ^
PTMTreeSearch.cpp:54:10: warning: unused variable 'tActiveNow' [-Wunused-variable]
  size_t tActiveNow = 0;
         ^
PTMTreeSearch.cpp:751:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
          m_vmodModificationsDB[resid].push_back(mod);
                               ^~~~~~
PTMTreeSearch.cpp:875:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_vmodModificationsDB[resid].push_back(mod);
                             ^~~~~~
PTMTreeSearch.cpp:1018:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_vmodModificationsDB[resid].push_back(mod);
                             ^~~~~~
PTMTreeSearch.cpp:1170:28: warning: array subscript is of type 'char' [-Wchar-subscripts]
      m_vmodModificationsDB[resid].push_back(mod);
                           ^~~~~~
PTMTreeSearch.cpp:1156:10: warning: unused variable 'pos' [-Wunused-variable]
  size_t pos = 0;
         ^
23 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c PTMTreeSearchScore.cpp -o PTMTreeSearchScore.o
In file included from PTMTreeSearchScore.cpp:13:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
In file included from PTMTreeSearchScore.cpp:14:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pOut;
                ^
                      []
./mmotif.h:295:16: note: allocated with 'new[]' here
                char *pOut = new char[256];
                             ^
PTMTreeSearchScore.cpp:369:19: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        dPTM = m_pdMods[m_pSeq[uiLevel]][uiModIt];
                                       ^~~~~~~~~~~~~~~~
PTMTreeSearchScore.cpp:373:31: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){ //this was the last modification, so delete this state
                                                          ^~~~~~~~~~~~~~~~
PTMTreeSearchScore.cpp:528:31: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){
                                                          ^~~~~~~~~~~~~~~~
PTMTreeSearchScore.cpp:568:31: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){
                                                          ^~~~~~~~~~~~~~~~
PTMTreeSearchScore.cpp:587:31: warning: array subscript is of 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:309:16: warning: unused variable 'ScoreOffset' [-Wunused-variable]
                unsigned int ScoreOffset;
                             ^
PTMTreeSearchScore.cpp:195:8: warning: unused variable 'active' [-Wunused-variable]
                bool active;
                     ^
PTMTreeSearchScore.cpp:624:16: warning: unused variable 'lValue' [-Wunused-variable]
        unsigned long lValue = 0;
                      ^
PTMTreeSearchScore.cpp:871:30: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                aaValue.m_dMod = m_pdMods[m_pSeq[i]][m_pBestGoal->m_uipPTMMap[i]-1];
                                                         ^~~~~~~~~~
PTMTreeSearchScore.cpp:895:49: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_dFixResidues[0] += m_pSeqUtilFrag->m_pdAaMod['['];
                                                              ^~~~
PTMTreeSearchScore.cpp:897:52: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_dFixResidues[0] += m_pSeqUtilFrag->m_pdAaFullMod['['];
                                                          ^~~~
PTMTreeSearchScore.cpp:903:49: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaMod[tC] + m_pSeqUtilFrag->m_pdAaFullMod[tC];
                                                              ^~~
PTMTreeSearchScore.cpp:903:85: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaMod[tC] + m_pSeqUtilFrag->m_pdAaFullMod[tC];
                                                                                                  ^~~
PTMTreeSearchScore.cpp:905:53: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaPrompt[tC];
                                                                         ^~~
PTMTreeSearchScore.cpp:921:49: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaMod[']'];
                                                              ^~~~
PTMTreeSearchScore.cpp:923:52: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaFullMod[']'];
                                                          ^~~~
PTMTreeSearchScore.cpp:952:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
                dValue += m_pSeqUtilFrag->m_pdAaMod['['];
                                                   ^~~~
PTMTreeSearchScore.cpp:954:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
        dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
                                               ^~~~
PTMTreeSearchScore.cpp:1029:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
                dValue += m_pSeqUtilFrag->m_pdAaMod['['];
                                                   ^~~~
PTMTreeSearchScore.cpp:1031:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
        dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
                                               ^~~~
PTMTreeSearchScore.cpp:1068:42: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_pfIntens[a] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
                                                       ^~~~~~~~~~~~
PTMTreeSearchScore.cpp:1116:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
                dValue += m_pSeqUtilFrag->m_pdAaMod['['];
                                                   ^~~~
PTMTreeSearchScore.cpp:1118:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
        dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
                                               ^~~~
PTMTreeSearchScore.cpp:1157:42: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_pfIntens[a] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
                                                       ^~~~~~~~~~~~
PTMTreeSearchScore.cpp:1183:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
                dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
                                                   ^~~~
PTMTreeSearchScore.cpp:1185:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
        dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
                                               ^~~~
PTMTreeSearchScore.cpp:1199:8: warning: unused variable 'fSub' [-Wunused-variable]
        float fSub = 0.0;
              ^
PTMTreeSearchScore.cpp:1259:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
                dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
                                                   ^~~~
PTMTreeSearchScore.cpp:1261:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
        dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
                                               ^~~~
PTMTreeSearchScore.cpp:1264:1: warning: '/*' within block comment [-Wcomment]
/*
^
PTMTreeSearchScore.cpp:1305:47: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                m_pfIntens[a-1] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                                          ^~~~~~~~~~~~
PTMTreeSearchScore.cpp:1314:46: warning: array subscript is of 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:1362:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
                dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
                                                   ^~~~
PTMTreeSearchScore.cpp:1364:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
        dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
                                               ^~~~
PTMTreeSearchScore.cpp:1366:1: warning: '/*' within block comment [-Wcomment]
/*
^
PTMTreeSearchScore.cpp:1405:45: warning: array subscript is of 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;
              ^
47 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c base64.cpp -o base64.o
base64.cpp:100:7: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
                int register a;
                    ^~~~~~~~~
base64.cpp:101:7: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
                int register b;
                    ^~~~~~~~~
base64.cpp:11:28: warning: unused variable 'b64_pad' [-Wunused-const-variable]
static const unsigned char b64_pad = '=';
                           ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c dataLoader.cpp -o dataLoader.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c loadmspectrum.cpp -o loadmspectrum.o
In file included from loadmspectrum.cpp:142:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
In file included from loadmspectrum.cpp:143:
./loadmspectrum.h:185:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pLine;
                ^
                      []
./loadmspectrum.h:176:17: note: allocated with 'new[]' here
                char *pLine = new char[tBuffer];
                              ^
loadmspectrum.cpp:498:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pLine;
        ^
              []
loadmspectrum.cpp:423:16: note: allocated with 'new[]' here
        char *pLine = new char[m_tSize];
                      ^
loadmspectrum.cpp:567:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pLine;
                ^
                      []
loadmspectrum.cpp:539:16: note: allocated with 'new[]' here
        char *pLine = new char[m_tSize];
                      ^
loadmspectrum.cpp:575:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pLine;
        ^
              []
loadmspectrum.cpp:539:16: note: allocated with 'new[]' here
        char *pLine = new char[m_tSize];
                      ^
loadmspectrum.cpp:698:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pLine;
        ^
              []
loadmspectrum.cpp:614:16: note: allocated with 'new[]' here
        char *pLine = new char[m_tSize];
                      ^
loadmspectrum.cpp:754:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pLine;
                ^
                      []
loadmspectrum.cpp:733:16: note: allocated with 'new[]' here
        char *pLine = new char[m_tSize];
                      ^
loadmspectrum.cpp:766:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pLine;
                ^
                      []
loadmspectrum.cpp:733:16: note: allocated with 'new[]' here
        char *pLine = new char[m_tSize];
                      ^
loadmspectrum.cpp:777:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pLine;
                ^
                      []
loadmspectrum.cpp:733:16: note: allocated with 'new[]' here
        char *pLine = new char[m_tSize];
                      ^
loadmspectrum.cpp:786:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pLine;
        ^
              []
loadmspectrum.cpp:733:16: note: allocated with 'new[]' here
        char *pLine = new char[m_tSize];
                      ^
loadmspectrum.cpp:820:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pLine;
        ^
              []
loadmspectrum.cpp:808:16: note: allocated with 'new[]' here
        char *pLine = new char[m_tSize];
                      ^
loadmspectrum.cpp:903:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pLine;
        ^
              []
loadmspectrum.cpp:834:16: note: allocated with 'new[]' here
        char *pLine = new char[m_tSize];
                      ^
loadmspectrum.cpp:958:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pLine;
                ^
                      []
loadmspectrum.cpp:937:16: note: allocated with 'new[]' here
        char *pLine = new char[m_tSize];
                      ^
loadmspectrum.cpp:971:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pLine;
                ^
                      []
loadmspectrum.cpp:937:16: note: allocated with 'new[]' here
        char *pLine = new char[m_tSize];
                      ^
loadmspectrum.cpp:980:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pLine;
        ^
              []
loadmspectrum.cpp:937:16: note: allocated with 'new[]' here
        char *pLine = new char[m_tSize];
                      ^
loadmspectrum.cpp:1011:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pLine;
        ^
              []
loadmspectrum.cpp:1002:16: note: allocated with 'new[]' here
        char *pLine = new char[m_tSize];
                      ^
loadmspectrum.cpp:1059:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pLine;
                        ^
                              []
loadmspectrum.cpp:1028:16: note: allocated with 'new[]' here
        char *pLine = new char[256];
                      ^
loadmspectrum.cpp:1114:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pLine;
        ^
              []
loadmspectrum.cpp:1028:16: note: allocated with 'new[]' here
        char *pLine = new char[256];
                      ^
loadmspectrum.cpp:1167:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pLine;
        ^
              []
loadmspectrum.cpp:1151:16: note: allocated with 'new[]' here
        char *pLine = new char[m_tSize];
                      ^
25 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c masscalc.cpp -o masscalc.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c mbiomlreport.cpp -o mbiomlreport.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c mpam.cpp -o mpam.o
In file included from mpam.cpp:137:
In file included from ./mprocess.h:143:
In file included from ./mspectrumcondition.h:153:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
In file included from mpam.cpp:138:
In file included from ./mscore.h:146:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pOut;
                ^
                      []
./mmotif.h:295:16: note: allocated with 'new[]' here
                char *pOut = new char[256];
                             ^
8 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c mplugin.cpp -o mplugin.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c mpmods.cpp -o mpmods.o
In file included from mpmods.cpp:137:
In file included from ./mprocess.h:143:
In file included from ./mspectrumcondition.h:153:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
In file included from mpmods.cpp:138:
In file included from ./mscore.h:146:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pOut;
                ^
                      []
./mmotif.h:295:16: note: allocated with 'new[]' here
                char *pOut = new char[256];
                             ^
8 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c mprocess.cpp -o mprocess.o
In file included from mprocess.cpp:156:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pOut;
                ^
                      []
./mmotif.h:295:16: note: allocated with 'new[]' here
                char *pOut = new char[256];
                             ^
In file included from mprocess.cpp:157:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
In file included from mprocess.cpp:158:
./loadmspectrum.h:185:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pLine;
                ^
                      []
./loadmspectrum.h:176:17: note: allocated with 'new[]' here
                char *pLine = new char[tBuffer];
                              ^
mprocess.cpp:440:7: warning: unused variable 'bC' [-Wunused-variable]
        bool bC = false;
             ^
mprocess.cpp:798:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pLine;
        ^
              []
mprocess.cpp:790:16: note: allocated with 'new[]' here
        char *pLine = new char[256];
                      ^
mprocess.cpp:1370:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pLine;
        ^
              []
mprocess.cpp:1361:16: note: allocated with 'new[]' here
        char *pLine = new char[256];
                      ^
mprocess.cpp:1768:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pOut;
                        ^
                              []
mprocess.cpp:1762:15: note: allocated with 'new[]' here
        char *pOut = new char[256];
                     ^
mprocess.cpp:1814:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pOut;
        ^
              []
mprocess.cpp:1762:15: note: allocated with 'new[]' here
        char *pOut = new char[256];
                     ^
mprocess.cpp:2273:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pLine;
        ^
              []
mprocess.cpp:2088:16: note: allocated with 'new[]' here
        char *pLine = new char[256];
                      ^
mprocess.cpp:2605:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pLine;
        ^
              []
mprocess.cpp:2573:16: note: allocated with 'new[]' here
        char *pLine = new char[256];
                      ^
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:2967:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete plCount;
        ^
              []
mprocess.cpp:2765:27: note: allocated with 'new[]' here
        unsigned long *plCount = new unsigned long[tMaxUid];
                                 ^
mprocess.cpp:2968:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pdExpect;
        ^
              []
mprocess.cpp:2764:21: note: allocated with 'new[]' here
        double *pdExpect = new double[tMaxUid];
                           ^
mprocess.cpp:3253:39: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_dNt = m_pScore->m_seqUtil.m_pdAaMod['['];
                                             ^~~~
mprocess.cpp:3254:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_dNtAve = m_pScore->m_seqUtilAvg.m_pdAaMod['['];
                                                   ^~~~
mprocess.cpp:3255:39: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_dNg = m_pScore->m_seqUtil.m_pdAaMod['n'];
                                             ^~~~
mprocess.cpp:3256:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_dNgAve = m_pScore->m_seqUtilAvg.m_pdAaMod['n'];
                                                   ^~~~
mprocess.cpp:3342:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                                m_pScore->m_seqUtil.m_pdAaMod['['] = dAcetyl;
                                                                             ^~~~
mprocess.cpp:3343:39: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                                m_pScore->m_seqUtilAvg.m_pdAaMod['['] = dAcetylAve;
                                                                                ^~~~
mprocess.cpp:3352:37: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                                        m_pScore->m_seqUtil.m_pdAaMod['['] = dAcetyl;
                                                                                     ^~~~
mprocess.cpp:3353:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                                        m_pScore->m_seqUtilAvg.m_pdAaMod['['] = dAcetylAve;
                                                                                        ^~~~
mprocess.cpp:3360:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                                m_pScore->m_seqUtil.m_pdAaMod['['] = m_dNt;
                                                                             ^~~~
mprocess.cpp:3361:39: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                                m_pScore->m_seqUtilAvg.m_pdAaMod['['] = m_dNtAve;
                                                                                ^~~~
mprocess.cpp:3366:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                                m_pScore->m_seqUtil.m_pdAaMod['n'] = dDeamidate;
                                                                             ^~~~
mprocess.cpp:3367:39: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                                m_pScore->m_seqUtilAvg.m_pdAaMod['n'] = dDeamidateAve;
                                                                                ^~~~
mprocess.cpp:3390:46: warning: '&&' within '||' [-Wlogical-op-parentheses]
                                                if(m_iCurrentRound == 1 && (m_bPermute && m_bCrcCheck || m_bPermuteHigh))       {
                                                                            ~~~~~~~~~~~^~~~~~~~~~~~~~ ~~
mprocess.cpp:3390:46: note: place parentheses around the '&&' expression to silence this warning
                                                if(m_iCurrentRound == 1 && (m_bPermute && m_bCrcCheck || m_bPermuteHigh))       {
                                                                                       ^
                                                                            (                        )
mprocess.cpp:3403:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                                m_pScore->m_seqUtil.m_pdAaMod['n'] = m_dNg;
                                                                             ^~~~
mprocess.cpp:3404:39: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                                m_pScore->m_seqUtilAvg.m_pdAaMod['n'] = m_dNgAve;
                                                                                ^~~~
mprocess.cpp:3415:35: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                        m_pScore->m_seqUtil.m_pdAaMod['['] = m_dNt;
                                                                     ^~~~
mprocess.cpp:3416:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                        m_pScore->m_seqUtilAvg.m_pdAaMod['['] = m_dNtAve;
                                                                        ^~~~
mprocess.cpp:3427:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                                                m_pScore->m_seqUtil.m_pdAaMod['['] = dAcetyl;
                                                                                             ^~~~
mprocess.cpp:3428:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                                                m_pScore->m_seqUtilAvg.m_pdAaMod['['] = dAcetylAve;
                                                                                                ^~~~
mprocess.cpp:3436:37: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                                        m_pScore->m_seqUtil.m_pdAaMod['n'] = dDeamidate;
                                                                                     ^~~~
mprocess.cpp:3437:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                                        m_pScore->m_seqUtilAvg.m_pdAaMod['n'] = dDeamidateAve;
                                                                                        ^~~~
mprocess.cpp:3459:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                                m_pScore->m_seqUtil.m_pdAaMod['['] = m_dNt;
                                                                             ^~~~
mprocess.cpp:3460:39: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                                m_pScore->m_seqUtilAvg.m_pdAaMod['['] = m_dNtAve;
                                                                                ^~~~
mprocess.cpp:3462:37: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                                        m_pScore->m_seqUtil.m_pdAaMod['n'] = m_dNg;
                                                                                     ^~~~
mprocess.cpp:3463:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                                        m_pScore->m_seqUtilAvg.m_pdAaMod['n'] = m_dNgAve;
                                                                                        ^~~~
mprocess.cpp:3520:34: warning: array subscript is of type 'char' [-Wchar-subscripts]
        if(m_pScore->m_seqUtil.m_pdAaMod['['] != 0.0 || !m_bQuickPyro)  {
                                        ^~~~
mprocess.cpp:3526:32: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_pScore->m_seqUtil.m_pdAaMod['['] = m_pyroState.m_dModMass;
                                             ^~~~
mprocess.cpp:3527:35: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_pScore->m_seqUtilAvg.m_pdAaMod['['] = -1.0*m_pScore->m_seqUtilAvg.m_dAmmonia;
                                                ^~~~
mprocess.cpp:3537:32: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_pScore->m_seqUtil.m_pdAaMod['['] = m_pyroState.m_dModMass;
                                             ^~~~
mprocess.cpp:3538:35: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_pScore->m_seqUtilAvg.m_pdAaMod['['] = -1.0*m_pScore->m_seqUtilAvg.m_dWater;
                                                ^~~~
mprocess.cpp:3546:63: warning: array subscript is of type 'char' [-Wchar-subscripts]
        else if(_c == 'C' && (long)(m_pScore->m_seqUtil.m_pdAaFullMod['C']) == 57)      {
                                                                     ^~~~
mprocess.cpp:3548:32: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_pScore->m_seqUtil.m_pdAaMod['['] = m_pyroState.m_dModMass;
                                             ^~~~
mprocess.cpp:3549:35: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_pScore->m_seqUtilAvg.m_pdAaMod['['] = -1.0*m_pScore->m_seqUtilAvg.m_dAmmonia;
                                                ^~~~
mprocess.cpp:3567:31: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_pScore->m_seqUtil.m_pdAaMod['['] = m_dNt;
                                     ^~~~
mprocess.cpp:3568:34: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_pScore->m_seqUtilAvg.m_pdAaMod['['] = m_dNtAve;
                                        ^~~~
mprocess.cpp:3759:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pValue;
                        ^
                              []
mprocess.cpp:3744:17: note: allocated with 'new[]' here
        char *pValue = new char[1028];
                       ^
mprocess.cpp:3775:6: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                                        delete pValue;
                                        ^
                                              []
mprocess.cpp:3744:17: note: allocated with 'new[]' here
        char *pValue = new char[1028];
                       ^
mprocess.cpp:3788:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                                delete pValue;
                                ^
                                      []
mprocess.cpp:3744:17: note: allocated with 'new[]' here
        char *pValue = new char[1028];
                       ^
mprocess.cpp:3810:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pValue;
                        ^
                              []
mprocess.cpp:3744:17: note: allocated with 'new[]' here
        char *pValue = new char[1028];
                       ^
mprocess.cpp:3815:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pValue;
        ^
              []
mprocess.cpp:3744:17: note: allocated with 'new[]' here
        char *pValue = new char[1028];
                       ^
mprocess.cpp:4843:14: warning: unused variable 'crc' [-Wunused-variable]
    uint64_t crc = INITIALCRC, part = 0;
             ^
61 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c mrefine.cpp -o mrefine.o
In file included from mrefine.cpp:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
In file included from mrefine.cpp:139:
In file included from ./mscore.h:146:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pOut;
                ^
                      []
./mmotif.h:295:16: note: allocated with 'new[]' here
                char *pOut = new char[256];
                             ^
mrefine.cpp:206:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pLine;
                ^
                      []
mrefine.cpp:197:17: note: allocated with 'new[]' here
                char *pLine = new char[256];
                              ^
mrefine.cpp:334:43: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_pProcess->m_pScore->m_seqUtil.m_pdAaMod['['] = 0.0;
                                                 ^~~~
mrefine.cpp:355:43: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_pProcess->m_pScore->m_seqUtil.m_pdAaMod[']'] = 0.0;
                                                 ^~~~
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;
               ^
13 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c mreport.cpp -o mreport.o
In file included from mreport.cpp:143:
In file included from ./saxsaphandler.h:140:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
In file included from mreport.cpp:147:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pOut;
                ^
                      []
./mmotif.h:295:16: note: allocated with 'new[]' here
                char *pOut = new char[256];
                             ^
mreport.cpp:264:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pLine;
        ^
              []
mreport.cpp:228:16: note: allocated with 'new[]' here
        char *pLine = new char[256];
                      ^
mreport.cpp:655:74: warning: array subscript is of type 'char' [-Wchar-subscripts]
                sprintf(pLine,"\t\n",cAa,_p.m_pdAaMass[cAa]);
                                                                                       ^~~~
mreport.cpp:667:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pLine;
        ^
              []
mreport.cpp:652:16: note: allocated with 'new[]' here
        char *pLine = new char[256];
                      ^
mreport.cpp:646:9: warning: unused variable 'a' [-Wunused-variable]
        size_t a = 0;
               ^
mreport.cpp:732:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pLine;
        ^
              []
mreport.cpp:717:16: note: allocated with 'new[]' here
        char *pLine = new char[256];
                      ^
mreport.cpp:874:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pLine;
        ^
              []
mreport.cpp:749:16: note: allocated with 'new[]' here
        char *pLine = new char[256];
                      ^
14 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c mscore.cpp -o mscore.o
In file included from mscore.cpp:152:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pOut;
                ^
                      []
./mmotif.h:295:16: note: allocated with 'new[]' here
                char *pOut = new char[256];
                             ^
In file included from mscore.cpp:153:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
mscore.cpp:301:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
                dValue += m_pSeqUtilFrag->m_pdAaMod['['];
                                                   ^~~~
mscore.cpp:303:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
        dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
                                               ^~~~
mscore.cpp:372:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
                dValue += m_pSeqUtilFrag->m_pdAaMod['['];
                                                   ^~~~
mscore.cpp:374:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
        dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
                                               ^~~~
mscore.cpp:450:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
                dValue += m_pSeqUtilFrag->m_pdAaMod['['];
                                                   ^~~~
mscore.cpp:452:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
        dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
                                               ^~~~
mscore.cpp:514:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
                dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
                                                   ^~~~
mscore.cpp:516:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
        dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
                                               ^~~~
mscore.cpp:586:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
                dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
                                                   ^~~~
mscore.cpp:588:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
        dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
                                               ^~~~
mscore.cpp:678:38: warning: array subscript is of type 'char' [-Wchar-subscripts]
                dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
                                                   ^~~~
mscore.cpp:680:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
        dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
                                               ^~~~
mscore.cpp:867:39: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_Term.initialize(m_seqUtil.m_pdAaMod['['],m_seqUtil.m_pdAaMod[']']);
                                             ^~~~
mscore.cpp:867:64: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_Term.initialize(m_seqUtil.m_pdAaMod['['],m_seqUtil.m_pdAaMod[']']);
                                                                      ^~~~
mscore.cpp:994:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
                if(a == '[' && m_seqUtil.m_pdAaFullMod['['] != 0.0)     {
                                                      ^~~~
mscore.cpp:997:51: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        aaValue.m_dMod = (float)m_seqUtil.m_pdAaFullMod['['];
                                                                       ^~~~
mscore.cpp:1001:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
                if(a == ']' && m_seqUtil.m_pdAaFullMod[']'] != 0.0)     {
                                                      ^~~~
mscore.cpp:1004:51: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        aaValue.m_dMod = (float)m_seqUtil.m_pdAaFullMod[']'];
                                                                       ^~~~
mscore.cpp:1244:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_Term.initialize(m_seqUtil.m_pdAaMod['['],m_seqUtil.m_pdAaMod[']']);
                                                     ^~~~
mscore.cpp:1244:65: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_Term.initialize(m_seqUtil.m_pdAaMod['['],m_seqUtil.m_pdAaMod[']']);
                                                                              ^~~~
mscore.cpp:1245:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_dSeqMH -= m_pSeqUtilFrag->m_pdAaMod['['];
                                                     ^~~~
mscore.cpp:1246:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_dSeqMH -= m_pSeqUtilFrag->m_pdAaMod[']'];
                                                     ^~~~
mscore.cpp:1259:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        m_dSeqMH += m_pSeqUtilFrag->m_pdAaMod['['];
                                                             ^~~~
mscore.cpp:1272:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        m_dSeqMH += m_pSeqUtilFrag->m_pdAaMod[']'];
                                                             ^~~~
mscore.cpp:1287:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        m_dSeqMH -= m_pSeqUtilFrag->m_pdAaMod['['];
                                                             ^~~~
mscore.cpp:1288:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        m_Term.initialize(m_seqUtil.m_pdAaMod['['],m_seqUtil.m_pdAaMod[']']);
                                                             ^~~~
mscore.cpp:1288:66: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        m_Term.initialize(m_seqUtil.m_pdAaMod['['],m_seqUtil.m_pdAaMod[']']);
                                                                                      ^~~~
mscore.cpp:1293:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_dSeqMH -= m_pSeqUtilFrag->m_pdAaMod['['];
                                                     ^~~~
mscore.cpp:1294:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_dSeqMH += m_pSeqUtilFrag->m_pdAaMod[']'];
                                                     ^~~~
mscore.cpp:1306:41: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        m_dSeqMH -= m_pSeqUtilFrag->m_pdAaMod[']'];
                                                             ^~~~
mscore.cpp:1307:47: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        m_Term.initialize(m_pSeqUtilFrag->m_pdAaMod['['],m_pSeqUtilFrag->m_pdAaMod[']']);
                                                                   ^~~~
mscore.cpp:1307:78: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        m_Term.initialize(m_pSeqUtilFrag->m_pdAaMod['['],m_pSeqUtilFrag->m_pdAaMod[']']);
                                                                                                  ^~~~
mscore.cpp:1310:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_dSeqMH += m_pSeqUtilFrag->m_pdAaMod['['];
                                                     ^~~~
mscore.cpp:1635:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        m_plAA['s'] = 0;
                              ^~~~
mscore.cpp:1636:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        m_plAA['t'] = 0;
                              ^~~~
mscore.cpp:1637:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        m_plAA['n'] = 0;
                              ^~~~
mscore.cpp:1638:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        m_plAA['q'] = 0;
                              ^~~~
mscore.cpp:1639:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        m_plAA['y'] = 0;
                              ^~~~
mscore.cpp:1650:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        m_State.m_bIsPossible = !(m_plAA['s'] + m_plAA['t'] + m_plAA['y'] > 3 || m_plAA['n'] + m_plAA['q'] > 3);
                                                        ^~~~
mscore.cpp:1650:50: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        m_State.m_bIsPossible = !(m_plAA['s'] + m_plAA['t'] + m_plAA['y'] > 3 || m_plAA['n'] + m_plAA['q'] > 3);
                                                                      ^~~~
mscore.cpp:1650:64: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        m_State.m_bIsPossible = !(m_plAA['s'] + m_plAA['t'] + m_plAA['y'] > 3 || m_plAA['n'] + m_plAA['q'] > 3);
                                                                                    ^~~~
mscore.cpp:1650:83: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        m_State.m_bIsPossible = !(m_plAA['s'] + m_plAA['t'] + m_plAA['y'] > 3 || m_plAA['n'] + m_plAA['q'] > 3);
                                                                                                       ^~~~
mscore.cpp:1650:97: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        m_State.m_bIsPossible = !(m_plAA['s'] + m_plAA['t'] + m_plAA['y'] > 3 || m_plAA['n'] + m_plAA['q'] > 3);
                                                                                                                     ^~~~
mscore.cpp:1912:39: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_Term.initialize(m_seqUtil.m_pdAaMod['['],m_seqUtil.m_pdAaMod[']']);
                                             ^~~~
mscore.cpp:1912:64: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_Term.initialize(m_seqUtil.m_pdAaMod['['],m_seqUtil.m_pdAaMod[']']);
                                                                      ^~~~
mscore.cpp:1951:34: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_dSeqMH += m_seqUtil.m_pdAaMod['['];
                                               ^~~~
mscore.cpp:1954:34: warning: array subscript is of type 'char' [-Wchar-subscripts]
                m_dSeqMH += m_seqUtil.m_pdAaMod[']'];
                                               ^~~~
mscore.cpp:1963:37: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_dSeqMH += m_seqUtil.m_pdAaFullMod['['];
                                           ^~~~
mscore.cpp:1964:37: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_dSeqMH += m_seqUtil.m_pdAaFullMod[']'];
                                           ^~~~
57 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c mscore_hrk.cpp -o mscore_hrk.o
In file included from mscore_hrk.cpp:24:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
In file included from mscore_hrk.cpp:25:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pOut;
                ^
                      []
./mmotif.h:295:16: note: allocated with 'new[]' here
                char *pOut = new char[256];
                             ^
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:544:54: warning: array subscript is of type 'char' [-Wchar-subscripts]
  if(m_Term.m_lN)       dValue += m_pSeqUtilFrag->m_pdAaMod['['];
                                                           ^~~~
mscore_hrk.cpp:545:42: warning: array subscript is of type 'char' [-Wchar-subscripts]
  dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
                                         ^~~~
mscore_hrk.cpp:550:10: warning: unused variable 'pfScore' [-Wunused-variable]
  float *pfScore = m_pSeqUtilFrag->m_pfAScore;
         ^
mscore_hrk.cpp:580:54: warning: array subscript is of type 'char' [-Wchar-subscripts]
  if(m_Term.m_lN)       dValue += m_pSeqUtilFrag->m_pdAaMod['['];
                                                           ^~~~
mscore_hrk.cpp:581:42: warning: array subscript is of type 'char' [-Wchar-subscripts]
  dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
                                         ^~~~
mscore_hrk.cpp:588:10: warning: unused variable 'pfScorePlus' [-Wunused-variable]
  float *pfScorePlus = m_pSeqUtilFrag->m_pfYScore;
         ^
mscore_hrk.cpp:587:10: warning: unused variable 'pfScore' [-Wunused-variable]
  float *pfScore = m_pSeqUtilFrag->m_pfBScore;
         ^
mscore_hrk.cpp:615:54: warning: array subscript is of type 'char' [-Wchar-subscripts]
  if(m_Term.m_lN)       dValue += m_pSeqUtilFrag->m_pdAaMod['['];
                                                           ^~~~
mscore_hrk.cpp:616:42: warning: array subscript is of type 'char' [-Wchar-subscripts]
  dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
                                         ^~~~
mscore_hrk.cpp:623:10: warning: unused variable 'pfScorePlus' [-Wunused-variable]
  float *pfScorePlus = m_pSeqUtilFrag->m_pfYScore;
         ^
mscore_hrk.cpp:622:10: warning: unused variable 'pfScore' [-Wunused-variable]
  float *pfScore = m_pSeqUtilFrag->m_pfBScore;
         ^
mscore_hrk.cpp:648:54: warning: array subscript is of type 'char' [-Wchar-subscripts]
  if(m_Term.m_lC)       dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
                                                           ^~~~
mscore_hrk.cpp:649:42: warning: array subscript is of type 'char' [-Wchar-subscripts]
  dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
                                         ^~~~
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:685:54: warning: array subscript is of type 'char' [-Wchar-subscripts]
  if(m_Term.m_lC)       dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
                                                           ^~~~
mscore_hrk.cpp:686:42: warning: array subscript is of type 'char' [-Wchar-subscripts]
  dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
                                         ^~~~
mscore_hrk.cpp:692:10: warning: unused variable 'pfScore' [-Wunused-variable]
  float *pfScore = m_pSeqUtilFrag->m_pfYScore;
         ^
mscore_hrk.cpp:691:9: warning: unused variable 'fSub' [-Wunused-variable]
  float fSub = 0.0;
        ^
mscore_hrk.cpp:693:10: warning: unused variable 'pfScoreMinus' [-Wunused-variable]
  float *pfScoreMinus = m_pSeqUtilFrag->m_pfBScore;
         ^
mscore_hrk.cpp:729:54: warning: array subscript is of type 'char' [-Wchar-subscripts]
  if(m_Term.m_lC)       dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
                                                           ^~~~
mscore_hrk.cpp:730:42: warning: array subscript is of type 'char' [-Wchar-subscripts]
  dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
                                         ^~~~
mscore_hrk.cpp:736:10: warning: unused variable 'pfScore' [-Wunused-variable]
  float *pfScore = m_pSeqUtilFrag->m_pfYScore;
         ^
mscore_hrk.cpp:735:9: warning: unused variable 'fSub' [-Wunused-variable]
  float fSub = 0.0;
        ^
mscore_hrk.cpp:737:10: warning: unused variable 'pfScoreMinus' [-Wunused-variable]
  float *pfScoreMinus = m_pSeqUtilFrag->m_pfBScore;
         ^
mscore_hrk.cpp:760:8: warning: unused variable 'lType' [-Wunused-variable]
  long lType = 0;
       ^
mscore_hrk.cpp:759:17: warning: unused variable 'lCount' [-Wunused-variable]
  unsigned long lCount = 0;
                ^
mscore_hrk.cpp:761:10: warning: unused variable 'b' [-Wunused-variable]
  size_t b = 0;
         ^
mscore_hrk.cpp:758:17: warning: unused variable 'a' [-Wunused-variable]
  unsigned long a = 0;
                ^
39 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c mscore_k.cpp -o mscore_k.o
In file included from mscore_k.cpp:24:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
In file included from mscore_k.cpp:25:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pOut;
                ^
                      []
./mmotif.h:295:16: note: allocated with 'new[]' here
                char *pOut = new char[256];
                             ^
mscore_k.cpp:378:15: warning: unused variable 'a' [-Wunused-variable]
unsigned long a = 0;
              ^
mscore_k.cpp:381:8: warning: unused variable 'b' [-Wunused-variable]
size_t b = 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:449:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod['['];
                                   ^~~~
mscore_k.cpp:451:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
                                       ^~~~
mscore_k.cpp:466:14: warning: unused variable 'dZ' [-Wunused-variable]
const double dZ = (double)_c;
             ^
mscore_k.cpp:505:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod['['];
                                   ^~~~
mscore_k.cpp:507:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
                                       ^~~~
mscore_k.cpp:529:42: warning: array subscript is of 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:567:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod['['];
                                   ^~~~
mscore_k.cpp:569:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod['['];
                                       ^~~~
mscore_k.cpp:591:42: warning: array subscript is of 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:615:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
                                   ^~~~
mscore_k.cpp:617:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
                                       ^~~~
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:673:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
                                   ^~~~
mscore_k.cpp:675:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
                                       ^~~~
mscore_k.cpp:677:1: warning: '/*' within block comment [-Wcomment]
/*
^
mscore_k.cpp:706:43: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                          ^~~~~~~~~~~~
mscore_k.cpp:712:43: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                          ^~~~~~~~~~~~
mscore_k.cpp:694:8: warning: unused variable 'dZ' [-Wunused-variable]
double dZ = (double)_c;
       ^
mscore_k.cpp:684:7: warning: unused variable 'fSub' [-Wunused-variable]
float fSub = 0.0;
      ^
mscore_k.cpp:749:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaMod[']'];
                                   ^~~~
mscore_k.cpp:751:40: warning: array subscript is of type 'char' [-Wchar-subscripts]
dValue += m_pSeqUtilFrag->m_pdAaFullMod[']'];
                                       ^~~~
mscore_k.cpp:753:1: warning: '/*' within block comment [-Wcomment]
/*
^
mscore_k.cpp:776:43: warning: array subscript is of type 'char' [-Wchar-subscripts]
m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                          ^~~~~~~~~~~~
mscore_k.cpp:779:43: warning: array subscript is of 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;
      ^
40 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c mscore_tandem.cpp -o mscore_tandem.o
In file included from mscore_tandem.cpp:135:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
In file included from mscore_tandem.cpp:136:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pOut;
                ^
                      []
./mmotif.h:295:16: note: allocated with 'new[]' here
                char *pOut = new char[256];
                             ^
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:581:16: warning: unused variable 'a' [-Wunused-variable]
        unsigned long a = 0;
                      ^
mscore_tandem.cpp:584:9: warning: unused variable 'b' [-Wunused-variable]
        size_t b = 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;
             ^
14 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c msequencecollection.cpp -o msequencecollection.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c msequenceserver.cpp -o msequenceserver.o
msequenceserver.cpp:605:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pLine;
        ^
              []
msequenceserver.cpp:561:16: note: allocated with 'new[]' here
        char *pLine = new char[lSize+1];
                      ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c msequtilities.cpp -o msequtilities.o
In file included from msequtilities.cpp:140:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pOut;
                ^
                      []
./mmotif.h:295:16: note: allocated with 'new[]' here
                char *pOut = new char[256];
                             ^
msequtilities.cpp:336:15: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_pdAaFullMod[']'] = 0.0;
                     ^~~~
msequtilities.cpp:337:15: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_pdAaFullMod['['] = 0.0;
                     ^~~~
msequtilities.cpp:384:11: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_pdAaMod['['] = 0.0;
                 ^~~~
msequtilities.cpp:385:11: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_pdAaMod[']'] = 0.0;
                 ^~~~
msequtilities.cpp:443:11: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_pdAaMod['['] = 0.0;
                 ^~~~
msequtilities.cpp:444:11: warning: array subscript is of type 'char' [-Wchar-subscripts]
        m_pdAaMod[']'] = 0.0;
                 ^~~~
msequtilities.cpp:488:19: warning: array subscript is of type 'char' [-Wchar-subscripts]
        if(fabs(m_pdAaMod['t']-79.966331) < 0.1)        {
                         ^~~~
msequtilities.cpp:492:19: warning: array subscript is of type 'char' [-Wchar-subscripts]
        if(fabs(m_pdAaMod['s']-79.966331) < 0.1)        {
                         ^~~~
msequtilities.cpp:496:19: warning: array subscript is of type 'char' [-Wchar-subscripts]
        if(fabs(m_pdAaMod['y']-79.966331) < 0.1)        {
                         ^~~~
msequtilities.cpp:533:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pString;
        ^
              []
msequtilities.cpp:517:18: note: allocated with 'new[]' here
        char *pString = new char[_s.m_strSeq.size()+1];
                        ^
msequtilities.cpp:615:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['a'] = pdValue['A'] = m_calc.calcMass("C3H5ON");
                       ^~~~
msequtilities.cpp:615:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['a'] = pdValue['A'] = m_calc.calcMass("C3H5ON");
                                      ^~~~
msequtilities.cpp:616:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['a'] = pValue['A'] = (float)pdValue['A'];
                      ^~~~
msequtilities.cpp:616:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['a'] = pValue['A'] = (float)pdValue['A'];
                                    ^~~~
msequtilities.cpp:616:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['a'] = pValue['A'] = (float)pdValue['A'];
                                                          ^~~~
msequtilities.cpp:618:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['b'] = pdValue['B'] = m_calc.calcMass("C4H6O2N2");      // Same as N
                       ^~~~
msequtilities.cpp:618:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['b'] = pdValue['B'] = m_calc.calcMass("C4H6O2N2");      // Same as N
                                      ^~~~
msequtilities.cpp:619:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['b'] = pValue['B'] = (float)pdValue['B'];
                      ^~~~
msequtilities.cpp:619:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['b'] = pValue['B'] = (float)pdValue['B'];
                                    ^~~~
msequtilities.cpp:619:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['b'] = pValue['B'] = (float)pdValue['B'];
                                                          ^~~~
msequtilities.cpp:621:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['c'] = pdValue['C'] = m_calc.calcMass("C3H5ONS");
                       ^~~~
msequtilities.cpp:621:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['c'] = pdValue['C'] = m_calc.calcMass("C3H5ONS");
                                      ^~~~
msequtilities.cpp:622:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['c'] = pValue['C'] = (float)pdValue['C'];
                      ^~~~
msequtilities.cpp:622:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['c'] = pValue['C'] = (float)pdValue['C'];
                                    ^~~~
msequtilities.cpp:622:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['c'] = pValue['C'] = (float)pdValue['C'];
                                                          ^~~~
msequtilities.cpp:624:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['d'] = pdValue['D'] = m_calc.calcMass("C4H5O3N");
                       ^~~~
msequtilities.cpp:624:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['d'] = pdValue['D'] = m_calc.calcMass("C4H5O3N");
                                      ^~~~
msequtilities.cpp:625:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['d'] = pValue['D'] = (float)pdValue['D'];
                      ^~~~
msequtilities.cpp:625:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['d'] = pValue['D'] = (float)pdValue['D'];
                                    ^~~~
msequtilities.cpp:625:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['d'] = pValue['D'] = (float)pdValue['D'];
                                                          ^~~~
msequtilities.cpp:627:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['e'] = pdValue['E'] = m_calc.calcMass("C5H7O3N");
                       ^~~~
msequtilities.cpp:627:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['e'] = pdValue['E'] = m_calc.calcMass("C5H7O3N");
                                      ^~~~
msequtilities.cpp:628:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['e'] = pValue['E'] = (float)pdValue['E'];
                      ^~~~
msequtilities.cpp:628:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['e'] = pValue['E'] = (float)pdValue['E'];
                                    ^~~~
msequtilities.cpp:628:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['e'] = pValue['E'] = (float)pdValue['E'];
                                                          ^~~~
msequtilities.cpp:630:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['f'] = pdValue['F'] = m_calc.calcMass("C9H9ON");
                       ^~~~
msequtilities.cpp:630:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['f'] = pdValue['F'] = m_calc.calcMass("C9H9ON");
                                      ^~~~
msequtilities.cpp:631:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['f'] = pValue['F'] = (float)pdValue['F'];
                      ^~~~
msequtilities.cpp:631:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['f'] = pValue['F'] = (float)pdValue['F'];
                                    ^~~~
msequtilities.cpp:631:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['f'] = pValue['F'] = (float)pdValue['F'];
                                                          ^~~~
msequtilities.cpp:633:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['g'] = pdValue['G'] = m_calc.calcMass("C2H3ON");
                       ^~~~
msequtilities.cpp:633:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['g'] = pdValue['G'] = m_calc.calcMass("C2H3ON");
                                      ^~~~
msequtilities.cpp:634:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['g'] = pValue['G'] = (float)pdValue['G'];
                      ^~~~
msequtilities.cpp:634:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['g'] = pValue['G'] = (float)pdValue['G'];
                                    ^~~~
msequtilities.cpp:634:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['g'] = pValue['G'] = (float)pdValue['G'];
                                                          ^~~~
msequtilities.cpp:636:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['h'] = pdValue['H'] = m_calc.calcMass("C6H7ON3");
                       ^~~~
msequtilities.cpp:636:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['h'] = pdValue['H'] = m_calc.calcMass("C6H7ON3");
                                      ^~~~
msequtilities.cpp:637:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['h'] = pValue['H'] = (float)pdValue['H'];
                      ^~~~
msequtilities.cpp:637:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['h'] = pValue['H'] = (float)pdValue['H'];
                                    ^~~~
msequtilities.cpp:637:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['h'] = pValue['H'] = (float)pdValue['H'];
                                                          ^~~~
msequtilities.cpp:639:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['i'] = pdValue['I'] = m_calc.calcMass("C6H11ON");
                       ^~~~
msequtilities.cpp:639:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['i'] = pdValue['I'] = m_calc.calcMass("C6H11ON");
                                      ^~~~
msequtilities.cpp:640:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['i'] = pValue['I'] = (float)pdValue['I'];
                      ^~~~
msequtilities.cpp:640:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['i'] = pValue['I'] = (float)pdValue['I'];
                                    ^~~~
msequtilities.cpp:640:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['i'] = pValue['I'] = (float)pdValue['I'];
                                                          ^~~~
msequtilities.cpp:642:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['j'] = pdValue['J'] = 0.0;
                       ^~~~
msequtilities.cpp:642:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['j'] = pdValue['J'] = 0.0;
                                      ^~~~
msequtilities.cpp:643:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['j'] = pValue['J'] = (float)pdValue['J'];
                      ^~~~
msequtilities.cpp:643:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['j'] = pValue['J'] = (float)pdValue['J'];
                                    ^~~~
msequtilities.cpp:643:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['j'] = pValue['J'] = (float)pdValue['J'];
                                                          ^~~~
msequtilities.cpp:645:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['k'] = pdValue['K'] = m_calc.calcMass("C6H12ON2");
                       ^~~~
msequtilities.cpp:645:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['k'] = pdValue['K'] = m_calc.calcMass("C6H12ON2");
                                      ^~~~
msequtilities.cpp:646:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['k'] = pValue['K'] = (float)pdValue['K'];
                      ^~~~
msequtilities.cpp:646:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['k'] = pValue['K'] = (float)pdValue['K'];
                                    ^~~~
msequtilities.cpp:646:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['k'] = pValue['K'] = (float)pdValue['K'];
                                                          ^~~~
msequtilities.cpp:648:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['l'] = pdValue['L'] = m_calc.calcMass("C6H11ON");
                       ^~~~
msequtilities.cpp:648:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['l'] = pdValue['L'] = m_calc.calcMass("C6H11ON");
                                      ^~~~
msequtilities.cpp:649:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['l'] = pValue['L'] = (float)pdValue['L'];
                      ^~~~
msequtilities.cpp:649:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['l'] = pValue['L'] = (float)pdValue['L'];
                                    ^~~~
msequtilities.cpp:649:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['l'] = pValue['L'] = (float)pdValue['L'];
                                                          ^~~~
msequtilities.cpp:651:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['m'] = pdValue['M'] = m_calc.calcMass("C5H9ONS");
                       ^~~~
msequtilities.cpp:651:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['m'] = pdValue['M'] = m_calc.calcMass("C5H9ONS");
                                      ^~~~
msequtilities.cpp:652:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['m'] = pValue['M'] = (float)pdValue['M'];
                      ^~~~
msequtilities.cpp:652:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['m'] = pValue['M'] = (float)pdValue['M'];
                                    ^~~~
msequtilities.cpp:652:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['m'] = pValue['M'] = (float)pdValue['M'];
                                                          ^~~~
msequtilities.cpp:654:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['n'] = pdValue['N'] = m_calc.calcMass("C4H6O2N2");
                       ^~~~
msequtilities.cpp:654:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['n'] = pdValue['N'] = m_calc.calcMass("C4H6O2N2");
                                      ^~~~
msequtilities.cpp:655:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['n'] = pValue['N'] = (float)pdValue['N'];
                      ^~~~
msequtilities.cpp:655:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['n'] = pValue['N'] = (float)pdValue['N'];
                                    ^~~~
msequtilities.cpp:655:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['n'] = pValue['N'] = (float)pdValue['N'];
                                                          ^~~~
msequtilities.cpp:657:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['o'] = pdValue['O'] = m_calc.calcMass("C4H6O2N2");      // Same as N
                       ^~~~
msequtilities.cpp:657:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['o'] = pdValue['O'] = m_calc.calcMass("C4H6O2N2");      // Same as N
                                      ^~~~
msequtilities.cpp:658:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['o'] = pValue['O'] = (float)pdValue['O'];
                      ^~~~
msequtilities.cpp:658:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['o'] = pValue['O'] = (float)pdValue['O'];
                                    ^~~~
msequtilities.cpp:658:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['o'] = pValue['O'] = (float)pdValue['O'];
                                                          ^~~~
msequtilities.cpp:660:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['p'] = pdValue['P'] = m_calc.calcMass("C5H7ON");
                       ^~~~
msequtilities.cpp:660:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['p'] = pdValue['P'] = m_calc.calcMass("C5H7ON");
                                      ^~~~
msequtilities.cpp:661:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['p'] = pValue['P'] = (float)pdValue['P'];
                      ^~~~
msequtilities.cpp:661:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['p'] = pValue['P'] = (float)pdValue['P'];
                                    ^~~~
msequtilities.cpp:661:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['p'] = pValue['P'] = (float)pdValue['P'];
                                                          ^~~~
msequtilities.cpp:663:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['q'] = pdValue['Q'] = m_calc.calcMass("C5H8O2N2");
                       ^~~~
msequtilities.cpp:663:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['q'] = pdValue['Q'] = m_calc.calcMass("C5H8O2N2");
                                      ^~~~
msequtilities.cpp:664:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['q'] = pValue['Q'] = (float)pdValue['Q'];
                      ^~~~
msequtilities.cpp:664:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['q'] = pValue['Q'] = (float)pdValue['Q'];
                                    ^~~~
msequtilities.cpp:664:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['q'] = pValue['Q'] = (float)pdValue['Q'];
                                                          ^~~~
msequtilities.cpp:666:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['r'] = pdValue['R'] = m_calc.calcMass("C6H12ON4");
                       ^~~~
msequtilities.cpp:666:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['r'] = pdValue['R'] = m_calc.calcMass("C6H12ON4");
                                      ^~~~
msequtilities.cpp:667:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['r'] = pValue['R'] = (float)pdValue['R'];
                      ^~~~
msequtilities.cpp:667:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['r'] = pValue['R'] = (float)pdValue['R'];
                                    ^~~~
msequtilities.cpp:667:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['r'] = pValue['R'] = (float)pdValue['R'];
                                                          ^~~~
msequtilities.cpp:669:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['s'] = pdValue['S'] = m_calc.calcMass("C3H5O2N");
                       ^~~~
msequtilities.cpp:669:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['s'] = pdValue['S'] = m_calc.calcMass("C3H5O2N");
                                      ^~~~
msequtilities.cpp:670:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['s'] = pValue['S'] = (float)pdValue['S'];
                      ^~~~
msequtilities.cpp:670:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['s'] = pValue['S'] = (float)pdValue['S'];
                                    ^~~~
msequtilities.cpp:670:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['s'] = pValue['S'] = (float)pdValue['S'];
                                                          ^~~~
msequtilities.cpp:672:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['t'] = pdValue['T'] = m_calc.calcMass("C4H7O2N");
                       ^~~~
msequtilities.cpp:672:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['t'] = pdValue['T'] = m_calc.calcMass("C4H7O2N");
                                      ^~~~
msequtilities.cpp:673:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['t'] = pValue['T'] = (float)pdValue['T'];
                      ^~~~
msequtilities.cpp:673:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['t'] = pValue['T'] = (float)pdValue['T'];
                                    ^~~~
msequtilities.cpp:673:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['t'] = pValue['T'] = (float)pdValue['T'];
                                                          ^~~~
msequtilities.cpp:675:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['u'] = pdValue['U'] = m_calc.calcMass("C3H5ONSe");      // selenocysteine
                       ^~~~
msequtilities.cpp:675:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['u'] = pdValue['U'] = m_calc.calcMass("C3H5ONSe");      // selenocysteine
                                      ^~~~
msequtilities.cpp:676:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['u'] = pValue['U'] = (float)pdValue['U'];
                      ^~~~
msequtilities.cpp:676:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['u'] = pValue['U'] = (float)pdValue['U'];
                                    ^~~~
msequtilities.cpp:676:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['u'] = pValue['U'] = (float)pdValue['U'];
                                                          ^~~~
msequtilities.cpp:678:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['v'] = pdValue['V'] = m_calc.calcMass("C5H9ON");
                       ^~~~
msequtilities.cpp:678:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['v'] = pdValue['V'] = m_calc.calcMass("C5H9ON");
                                      ^~~~
msequtilities.cpp:679:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['v'] = pValue['V'] = (float)pdValue['V'];
                      ^~~~
msequtilities.cpp:679:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['v'] = pValue['V'] = (float)pdValue['V'];
                                    ^~~~
msequtilities.cpp:679:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['v'] = pValue['V'] = (float)pdValue['V'];
                                                          ^~~~
msequtilities.cpp:681:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['w'] = pdValue['W'] = m_calc.calcMass("C11H10ON2");
                       ^~~~
msequtilities.cpp:681:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['w'] = pdValue['W'] = m_calc.calcMass("C11H10ON2");
                                      ^~~~
msequtilities.cpp:682:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['w'] = pValue['W'] = (float)pdValue['W'];
                      ^~~~
msequtilities.cpp:682:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['w'] = pValue['W'] = (float)pdValue['W'];
                                    ^~~~
msequtilities.cpp:682:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['w'] = pValue['W'] = (float)pdValue['W'];
                                                          ^~~~
msequtilities.cpp:684:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['x'] = pdValue['X'] = 111.060000;       // Why?
                       ^~~~
msequtilities.cpp:684:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['x'] = pdValue['X'] = 111.060000;       // Why?
                                      ^~~~
msequtilities.cpp:685:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['x'] = pValue['X'] = (float)pdValue['X'];
                      ^~~~
msequtilities.cpp:685:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['x'] = pValue['X'] = (float)pdValue['X'];
                                    ^~~~
msequtilities.cpp:685:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['x'] = pValue['X'] = (float)pdValue['X'];
                                                          ^~~~
msequtilities.cpp:687:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['y'] = pdValue['Y'] = m_calc.calcMass("C9H9O2N");
                       ^~~~
msequtilities.cpp:687:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['y'] = pdValue['Y'] = m_calc.calcMass("C9H9O2N");
                                      ^~~~
msequtilities.cpp:688:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['y'] = pValue['Y'] = (float)pdValue['Y'];
                      ^~~~
msequtilities.cpp:688:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['y'] = pValue['Y'] = (float)pdValue['Y'];
                                    ^~~~
msequtilities.cpp:688:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['y'] = pValue['Y'] = (float)pdValue['Y'];
                                                          ^~~~
msequtilities.cpp:690:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['z'] = pdValue['Z'] = m_calc.calcMass("C5H8O2N2");      // Same as Q
                       ^~~~
msequtilities.cpp:690:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['z'] = pdValue['Z'] = m_calc.calcMass("C5H8O2N2");      // Same as Q
                                      ^~~~
msequtilities.cpp:691:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['z'] = pValue['Z'] = (float)pdValue['Z'];
                      ^~~~
msequtilities.cpp:691:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['z'] = pValue['Z'] = (float)pdValue['Z'];
                                    ^~~~
msequtilities.cpp:691:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['z'] = pValue['Z'] = (float)pdValue['Z'];
                                                          ^~~~
msequtilities.cpp:693:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['b'] = pdValue['B'] = m_calc.calcMass("C10H21O2N3");    // Hypusine
                       ^~~~
msequtilities.cpp:693:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['b'] = pdValue['B'] = m_calc.calcMass("C10H21O2N3");    // Hypusine
                                      ^~~~
msequtilities.cpp:694:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['b'] = pValue['B'] = (float)pdValue['B'];
                      ^~~~
msequtilities.cpp:694:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['b'] = pValue['B'] = (float)pdValue['B'];
                                    ^~~~
msequtilities.cpp:694:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['b'] = pValue['B'] = (float)pdValue['B'];
                                                          ^~~~
msequtilities.cpp:705:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['a'] = pdValue['A'] = 71.0788;
                       ^~~~
msequtilities.cpp:705:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['a'] = pdValue['A'] = 71.0788;
                                      ^~~~
msequtilities.cpp:706:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['a'] = pValue['A'] = (float)pdValue['A'];
                      ^~~~
msequtilities.cpp:706:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['a'] = pValue['A'] = (float)pdValue['A'];
                                    ^~~~
msequtilities.cpp:706:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['a'] = pValue['A'] = (float)pdValue['A'];
                                                          ^~~~
msequtilities.cpp:708:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['b'] = pdValue['B'] = 114.1038; // Same as N
                       ^~~~
msequtilities.cpp:708:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['b'] = pdValue['B'] = 114.1038; // Same as N
                                      ^~~~
msequtilities.cpp:709:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['b'] = pValue['B'] = (float)pdValue['B'];
                      ^~~~
msequtilities.cpp:709:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['b'] = pValue['B'] = (float)pdValue['B'];
                                    ^~~~
msequtilities.cpp:709:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['b'] = pValue['B'] = (float)pdValue['B'];
                                                          ^~~~
msequtilities.cpp:711:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['c'] = pdValue['C'] = 103.1388;
                       ^~~~
msequtilities.cpp:711:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['c'] = pdValue['C'] = 103.1388;
                                      ^~~~
msequtilities.cpp:712:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['c'] = pValue['C'] = (float)pdValue['C'];
                      ^~~~
msequtilities.cpp:712:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['c'] = pValue['C'] = (float)pdValue['C'];
                                    ^~~~
msequtilities.cpp:712:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['c'] = pValue['C'] = (float)pdValue['C'];
                                                          ^~~~
msequtilities.cpp:714:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['d'] = pdValue['D'] = 115.0886;
                       ^~~~
msequtilities.cpp:714:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['d'] = pdValue['D'] = 115.0886;
                                      ^~~~
msequtilities.cpp:715:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['d'] = pValue['D'] = (float)pdValue['D'];
                      ^~~~
msequtilities.cpp:715:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['d'] = pValue['D'] = (float)pdValue['D'];
                                    ^~~~
msequtilities.cpp:715:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['d'] = pValue['D'] = (float)pdValue['D'];
                                                          ^~~~
msequtilities.cpp:717:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['e'] = pdValue['E'] = 129.1155;
                       ^~~~
msequtilities.cpp:717:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['e'] = pdValue['E'] = 129.1155;
                                      ^~~~
msequtilities.cpp:718:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['e'] = pValue['E'] = (float)pdValue['E'];
                      ^~~~
msequtilities.cpp:718:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['e'] = pValue['E'] = (float)pdValue['E'];
                                    ^~~~
msequtilities.cpp:718:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['e'] = pValue['E'] = (float)pdValue['E'];
                                                          ^~~~
msequtilities.cpp:720:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['f'] = pdValue['F'] = 147.1766;
                       ^~~~
msequtilities.cpp:720:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['f'] = pdValue['F'] = 147.1766;
                                      ^~~~
msequtilities.cpp:721:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['f'] = pValue['F'] = (float)pdValue['F'];
                      ^~~~
msequtilities.cpp:721:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['f'] = pValue['F'] = (float)pdValue['F'];
                                    ^~~~
msequtilities.cpp:721:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['f'] = pValue['F'] = (float)pdValue['F'];
                                                          ^~~~
msequtilities.cpp:723:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['g'] = pdValue['G'] = 57.0519;
                       ^~~~
msequtilities.cpp:723:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['g'] = pdValue['G'] = 57.0519;
                                      ^~~~
msequtilities.cpp:724:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['g'] = pValue['G'] = (float)pdValue['G'];
                      ^~~~
msequtilities.cpp:724:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['g'] = pValue['G'] = (float)pdValue['G'];
                                    ^~~~
msequtilities.cpp:724:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['g'] = pValue['G'] = (float)pdValue['G'];
                                                          ^~~~
msequtilities.cpp:726:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['h'] = pdValue['H'] = 137.1411;
                       ^~~~
msequtilities.cpp:726:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['h'] = pdValue['H'] = 137.1411;
                                      ^~~~
msequtilities.cpp:727:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['h'] = pValue['H'] = (float)pdValue['H'];
                      ^~~~
msequtilities.cpp:727:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['h'] = pValue['H'] = (float)pdValue['H'];
                                    ^~~~
msequtilities.cpp:727:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['h'] = pValue['H'] = (float)pdValue['H'];
                                                          ^~~~
msequtilities.cpp:729:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['i'] = pdValue['I'] = 113.1594;
                       ^~~~
msequtilities.cpp:729:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['i'] = pdValue['I'] = 113.1594;
                                      ^~~~
msequtilities.cpp:730:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['i'] = pValue['I'] = (float)pdValue['I'];
                      ^~~~
msequtilities.cpp:730:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['i'] = pValue['I'] = (float)pdValue['I'];
                                    ^~~~
msequtilities.cpp:730:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['i'] = pValue['I'] = (float)pdValue['I'];
                                                          ^~~~
msequtilities.cpp:732:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['j'] = pdValue['J'] = 0.0;
                       ^~~~
msequtilities.cpp:732:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['j'] = pdValue['J'] = 0.0;
                                      ^~~~
msequtilities.cpp:733:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['j'] = pValue['J'] = (float)pdValue['J'];
                      ^~~~
msequtilities.cpp:733:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['j'] = pValue['J'] = (float)pdValue['J'];
                                    ^~~~
msequtilities.cpp:733:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['j'] = pValue['J'] = (float)pdValue['J'];
                                                          ^~~~
msequtilities.cpp:735:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['k'] = pdValue['K'] = 128.1741;
                       ^~~~
msequtilities.cpp:735:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['k'] = pdValue['K'] = 128.1741;
                                      ^~~~
msequtilities.cpp:736:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['k'] = pValue['K'] = (float)pdValue['K'];
                      ^~~~
msequtilities.cpp:736:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['k'] = pValue['K'] = (float)pdValue['K'];
                                    ^~~~
msequtilities.cpp:736:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['k'] = pValue['K'] = (float)pdValue['K'];
                                                          ^~~~
msequtilities.cpp:738:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['l'] = pdValue['L'] = 113.1594;
                       ^~~~
msequtilities.cpp:738:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['l'] = pdValue['L'] = 113.1594;
                                      ^~~~
msequtilities.cpp:739:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['l'] = pValue['L'] = (float)pdValue['L'];
                      ^~~~
msequtilities.cpp:739:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['l'] = pValue['L'] = (float)pdValue['L'];
                                    ^~~~
msequtilities.cpp:739:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['l'] = pValue['L'] = (float)pdValue['L'];
                                                          ^~~~
msequtilities.cpp:741:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['m'] = pdValue['M'] = 131.1926;
                       ^~~~
msequtilities.cpp:741:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['m'] = pdValue['M'] = 131.1926;
                                      ^~~~
msequtilities.cpp:742:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['m'] = pValue['M'] = (float)pdValue['M'];
                      ^~~~
msequtilities.cpp:742:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['m'] = pValue['M'] = (float)pdValue['M'];
                                    ^~~~
msequtilities.cpp:742:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['m'] = pValue['M'] = (float)pdValue['M'];
                                                          ^~~~
msequtilities.cpp:744:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['n'] = pdValue['N'] = 114.1038;
                       ^~~~
msequtilities.cpp:744:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['n'] = pdValue['N'] = 114.1038;
                                      ^~~~
msequtilities.cpp:745:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['n'] = pValue['N'] = (float)pdValue['N'];
                      ^~~~
msequtilities.cpp:745:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['n'] = pValue['N'] = (float)pdValue['N'];
                                    ^~~~
msequtilities.cpp:745:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['n'] = pValue['N'] = (float)pdValue['N'];
                                                          ^~~~
msequtilities.cpp:747:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['o'] = pdValue['O'] = 114.1038; // Same as N
                       ^~~~
msequtilities.cpp:747:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['o'] = pdValue['O'] = 114.1038; // Same as N
                                      ^~~~
msequtilities.cpp:748:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['o'] = pValue['O'] = (float)pdValue['O'];
                      ^~~~
msequtilities.cpp:748:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['o'] = pValue['O'] = (float)pdValue['O'];
                                    ^~~~
msequtilities.cpp:748:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['o'] = pValue['O'] = (float)pdValue['O'];
                                                          ^~~~
msequtilities.cpp:750:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['p'] = pdValue['P'] = 97.1167;
                       ^~~~
msequtilities.cpp:750:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['p'] = pdValue['P'] = 97.1167;
                                      ^~~~
msequtilities.cpp:751:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['p'] = pValue['P'] = (float)pdValue['P'];
                      ^~~~
msequtilities.cpp:751:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['p'] = pValue['P'] = (float)pdValue['P'];
                                    ^~~~
msequtilities.cpp:751:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['p'] = pValue['P'] = (float)pdValue['P'];
                                                          ^~~~
msequtilities.cpp:753:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['q'] = pdValue['Q'] = 128.1307;
                       ^~~~
msequtilities.cpp:753:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['q'] = pdValue['Q'] = 128.1307;
                                      ^~~~
msequtilities.cpp:754:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['q'] = pValue['Q'] = (float)pdValue['Q'];
                      ^~~~
msequtilities.cpp:754:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['q'] = pValue['Q'] = (float)pdValue['Q'];
                                    ^~~~
msequtilities.cpp:754:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['q'] = pValue['Q'] = (float)pdValue['Q'];
                                                          ^~~~
msequtilities.cpp:756:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['r'] = pdValue['R'] = 156.1875;
                       ^~~~
msequtilities.cpp:756:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['r'] = pdValue['R'] = 156.1875;
                                      ^~~~
msequtilities.cpp:757:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['r'] = pValue['R'] = (float)pdValue['R'];
                      ^~~~
msequtilities.cpp:757:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['r'] = pValue['R'] = (float)pdValue['R'];
                                    ^~~~
msequtilities.cpp:757:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['r'] = pValue['R'] = (float)pdValue['R'];
                                                          ^~~~
msequtilities.cpp:759:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['s'] = pdValue['S'] = 87.0782;
                       ^~~~
msequtilities.cpp:759:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['s'] = pdValue['S'] = 87.0782;
                                      ^~~~
msequtilities.cpp:760:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['s'] = pValue['S'] = (float)pdValue['S'];
                      ^~~~
msequtilities.cpp:760:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['s'] = pValue['S'] = (float)pdValue['S'];
                                    ^~~~
msequtilities.cpp:760:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['s'] = pValue['S'] = (float)pdValue['S'];
                                                          ^~~~
msequtilities.cpp:762:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['t'] = pdValue['T'] = 101.1051;
                       ^~~~
msequtilities.cpp:762:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['t'] = pdValue['T'] = 101.1051;
                                      ^~~~
msequtilities.cpp:763:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['t'] = pValue['T'] = (float)pdValue['T'];
                      ^~~~
msequtilities.cpp:763:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['t'] = pValue['T'] = (float)pdValue['T'];
                                    ^~~~
msequtilities.cpp:763:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['t'] = pValue['T'] = (float)pdValue['T'];
                                                          ^~~~
msequtilities.cpp:765:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['u'] = pdValue['U'] = 103.1388 - 32.066 + 78.96;        // selenocysteine
                       ^~~~
msequtilities.cpp:765:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['u'] = pdValue['U'] = 103.1388 - 32.066 + 78.96;        // selenocysteine
                                      ^~~~
msequtilities.cpp:766:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['u'] = pValue['U'] = (float)pdValue['U'];
                      ^~~~
msequtilities.cpp:766:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['u'] = pValue['U'] = (float)pdValue['U'];
                                    ^~~~
msequtilities.cpp:766:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['u'] = pValue['U'] = (float)pdValue['U'];
                                                          ^~~~
msequtilities.cpp:768:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['v'] = pdValue['V'] = 99.1326;
                       ^~~~
msequtilities.cpp:768:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['v'] = pdValue['V'] = 99.1326;
                                      ^~~~
msequtilities.cpp:769:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['v'] = pValue['V'] = (float)pdValue['V'];
                      ^~~~
msequtilities.cpp:769:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['v'] = pValue['V'] = (float)pdValue['V'];
                                    ^~~~
msequtilities.cpp:769:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['v'] = pValue['V'] = (float)pdValue['V'];
                                                          ^~~~
msequtilities.cpp:771:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['w'] = pdValue['W'] = 186.2132;
                       ^~~~
msequtilities.cpp:771:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['w'] = pdValue['W'] = 186.2132;
                                      ^~~~
msequtilities.cpp:772:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['w'] = pValue['W'] = (float)pdValue['W'];
                      ^~~~
msequtilities.cpp:772:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['w'] = pValue['W'] = (float)pdValue['W'];
                                    ^~~~
msequtilities.cpp:772:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['w'] = pValue['W'] = (float)pdValue['W'];
                                                          ^~~~
msequtilities.cpp:774:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['x'] = pdValue['X'] = 113.1594; // Why?
                       ^~~~
msequtilities.cpp:774:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['x'] = pdValue['X'] = 113.1594; // Why?
                                      ^~~~
msequtilities.cpp:775:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['x'] = pValue['X'] = (float)pdValue['X'];
                      ^~~~
msequtilities.cpp:775:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['x'] = pValue['X'] = (float)pdValue['X'];
                                    ^~~~
msequtilities.cpp:775:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['x'] = pValue['X'] = (float)pdValue['X'];
                                                          ^~~~
msequtilities.cpp:777:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['y'] = pdValue['Y'] = 163.1760;
                       ^~~~
msequtilities.cpp:777:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['y'] = pdValue['Y'] = 163.1760;
                                      ^~~~
msequtilities.cpp:778:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['y'] = pValue['Y'] = (float)pdValue['Y'];
                      ^~~~
msequtilities.cpp:778:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['y'] = pValue['Y'] = (float)pdValue['Y'];
                                    ^~~~
msequtilities.cpp:778:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['y'] = pValue['Y'] = (float)pdValue['Y'];
                                                          ^~~~
msequtilities.cpp:780:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['z'] = pdValue['Z'] = 128.1307; // Same as Q
                       ^~~~
msequtilities.cpp:780:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pdValue['z'] = pdValue['Z'] = 128.1307; // Same as Q
                                      ^~~~
msequtilities.cpp:781:9: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['z'] = pValue['Z'] = (float)pdValue['Z'];
                      ^~~~
msequtilities.cpp:781:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['z'] = pValue['Z'] = (float)pdValue['Z'];
                                    ^~~~
msequtilities.cpp:781:45: warning: array subscript is of type 'char' [-Wchar-subscripts]
                pValue['z'] = pValue['Z'] = (float)pdValue['Z'];
                                                          ^~~~
276 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c mspectrumcondition.cpp -o mspectrumcondition.o
In file included from mspectrumcondition.cpp:153:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pOut;
                ^
                      []
./mmotif.h:295:16: note: allocated with 'new[]' here
                char *pOut = new char[256];
                             ^
In file included from mspectrumcondition.cpp:154:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
8 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c mtermmods.cpp -o mtermmods.o
In file included from mtermmods.cpp:137:
In file included from ./mprocess.h:143:
In file included from ./mspectrumcondition.h:153:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
In file included from mtermmods.cpp:138:
In file included from ./mscore.h:146:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pOut;
                ^
                      []
./mmotif.h:295:16: note: allocated with 'new[]' here
                char *pOut = new char[256];
                             ^
8 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c mxxcleavage.cpp -o mxxcleavage.o
In file included from mxxcleavage.cpp:137:
In file included from ./mprocess.h:143:
In file included from ./mspectrumcondition.h:153:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
In file included from mxxcleavage.cpp:138:
In file included from ./mscore.h:146:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pOut;
                ^
                      []
./mmotif.h:295:16: note: allocated with 'new[]' here
                char *pOut = new char[256];
                             ^
8 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c saxbiomlhandler.cpp -o saxbiomlhandler.o
In file included from saxbiomlhandler.cpp:140:
In file included from ./saxbiomlhandler.h:140:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c saxgamlhandler.cpp -o saxgamlhandler.o
In file included from saxgamlhandler.cpp:139:
In file included from ./saxgamlhandler.h:140:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c saxhandler.cpp -o saxhandler.o
In file included from saxhandler.cpp:132:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
saxhandler.cpp:335:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pLine;
                ^
                      []
saxhandler.cpp:307:17: note: allocated with 'new[]' here
                char *pLine = new char[m_strData.size()+1];
                              ^
8 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c saxmodhandler.cpp -o saxmodhandler.o
In file included from saxmodhandler.cpp:140:
In file included from ./saxmodhandler.h:140:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c saxmzdatahandler.cpp -o saxmzdatahandler.o
In file included from saxmzdatahandler.cpp:28:
In file included from ./saxmzdatahandler.h:4:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c saxmzmlhandler.cpp -o saxmzmlhandler.o
In file included from saxmzmlhandler.cpp:33:
In file included from ./saxmzmlhandler.h:4:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c saxmzxmlhandler.cpp -o saxmzxmlhandler.o
In file included from saxmzxmlhandler.cpp:20:
In file included from ./saxmzxmlhandler.h:4:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c saxsaphandler.cpp -o saxsaphandler.o
In file included from saxsaphandler.cpp:140:
In file included from ./saxsaphandler.h:140:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c saxtandeminputhandler.cpp -o saxtandeminputhandler.o
In file included from saxtandeminputhandler.cpp:139:
In file included from ./saxtandeminputhandler.h:140:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c saxtaxhandler.cpp -o saxtaxhandler.o
In file included from saxtaxhandler.cpp:139:
In file included from ./saxtaxhandler.h:140:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c stdafx.cpp -o stdafx.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c tandem.cpp -o tandem.o
In file included from tandem.cpp:143:
In file included from ./tandem.h:14:
In file included from ./msequtilities.h:142:
./mmotif.h:370:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pOut;
                ^
                      []
./mmotif.h:295:16: note: allocated with 'new[]' here
                char *pOut = new char[256];
                             ^
In file included from tandem.cpp:143:
In file included from ./tandem.h:15:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
tandem.cpp:225:62: warning: if statement has empty body [-Wempty-body]
        if(!pProcess[0]->load(param, peptide, saps, mods, spectrum));
                                                                    ^
tandem.cpp:225:62: note: put the semicolon on a separate line to silence this warning
tandem.cpp:323:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                                delete pProcess;
                                ^
                                      []
tandem.cpp:188:24: note: allocated with 'new[]' here
        mprocess **pProcess = new mprocess*[lMaxThreads];
                              ^
tandem.cpp:404:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pS;
        ^
              []
tandem.cpp:221:13: note: allocated with 'new[]' here
        char *pS = new char[1024];
                   ^
tandem.cpp:720:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pProcess;
        ^
              []
tandem.cpp:188:24: note: allocated with 'new[]' here
        mprocess **pProcess = new mprocess*[lMaxThreads];
                              ^
tandem.cpp:721:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pId;
        ^
              []
tandem.cpp:199:13: note: allocated with 'new[]' here
        int *pId = new int[lMaxThreads];
                   ^
tandem.cpp:722:2: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
        delete pHandle;
        ^
              []
tandem.cpp:200:17: note: allocated with 'new[]' here
        int *pHandle = new int[lMaxThreads];
                       ^
tandem.cpp:277:12: warning: unused variable 'tCount' [-Wunused-variable]
    size_t tCount = pProcess[0]->m_vSpectra.size();
           ^
15 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c xmlparameter.cpp -o xmlparameter.o
In file included from xmlparameter.cpp:144:
In file included from ./saxtandeminputhandler.h:140:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c xmltaxonomy.cpp -o xmltaxonomy.o
In file included from xmltaxonomy.cpp:160:
In file included from ./saxtaxhandler.h:140:
In file included from ./saxhandler.h:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:391:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete plValues;
                ^
                      []
./mhistogram.h:345:19: note: allocated with 'new[]' here
                int *plValues = new int[m_lLength];
                                ^
./mhistogram.h:392:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pTempList;
                ^
                      []
./mhistogram.h:349:21: note: allocated with 'new[]' here
                int *pTempList =  new int[m_lLength];
                                  ^
./mhistogram.h:469:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfX;
                        ^
                              []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:470:4: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                        delete pfT;
                        ^
                              []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:486:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfX; 
                ^
                      []
./mhistogram.h:417:16: note: allocated with 'new[]' here
                float *pfX = new float[m_lLength];
                             ^
./mhistogram.h:487:3: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
                delete pfT;
                ^
                      []
./mhistogram.h:418:16: note: allocated with 'new[]' here
                float *pfT = new float[m_lLength];
                             ^
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
7 warnings generated.
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/rTANDEM.buildbin-libdir/00LOCK-rTANDEM/00new/rTANDEM/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rTANDEM)


>>>>>>> 
>>>>>>> FIXING LINKS FOR rTANDEM.buildbin-libdir/rTANDEM/libs//rTANDEM.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "rTANDEM.buildbin-libdir/rTANDEM/libs//rTANDEM.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "rTANDEM.buildbin-libdir/rTANDEM/libs//rTANDEM.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "rTANDEM.buildbin-libdir/rTANDEM/libs//rTANDEM.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "rTANDEM.buildbin-libdir/rTANDEM/libs//rTANDEM.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "rTANDEM.buildbin-libdir/rTANDEM/libs//rTANDEM.so"
BUILD BIN report for rTANDEM on celaya2

Summary

Command output
