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BioC 2.14: CHECK report for rTANDEM on morelia

This page was generated on 2014-10-08 09:06:02 -0700 (Wed, 08 Oct 2014).

Package 692/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rTANDEM 1.4.0
Frederic Fournier
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/rTANDEM
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: rTANDEM
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rTANDEM_1.4.0.tar.gz
StartedAt: 2014-10-08 01:23:27 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 01:26:25 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 177.5 seconds
RetCode: 0
Status:  OK 
CheckDir: rTANDEM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rTANDEM_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/rTANDEM.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rTANDEM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rTANDEM’ version ‘1.4.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rTANDEM’ can be installed ... [134s/134s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘XML’ ‘data.table’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/Users/biocbuild/bbs-2.14-bioc/meat/rTANDEM.Rcheck/rTANDEM/libs/rTANDEM.so’:
  Found non-API call to R: ‘R_CStackLimit’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/rTANDEM.Rcheck/00check.log’
for details.

rTANDEM.Rcheck/00install.out:

* installing *source* package ‘rTANDEM’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
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:1003:18: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
      while (pos = m_strResidues.find(',')>m_strResidues.npos){
             ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearch.cpp:1003:18: note: place parentheses around the assignment to silence this warning
      while (pos = m_strResidues.find(',')>m_strResidues.npos){
                 ^
             (                                               )
PTMTreeSearch.cpp:1003:18: note: use '==' to turn this assignment into an equality comparison
      while (pos = m_strResidues.find(',')>m_strResidues.npos){
                 ^
                 ==
PTMTreeSearch.cpp:1006:18: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
      while (pos = m_strResidues.find(' ')>m_strResidues.npos){
             ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
PTMTreeSearch.cpp:1006:18: note: place parentheses around the assignment to silence this warning
      while (pos = m_strResidues.find(' ')>m_strResidues.npos){
                 ^
             (                                               )
PTMTreeSearch.cpp:1006:18: note: use '==' to turn this assignment into an equality comparison
      while (pos = m_strResidues.find(' ')>m_strResidues.npos){
                 ^
                 ==
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;
         ^
18 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c PTMTreeSearchScore.cpp -o PTMTreeSearchScore.o
In file included from PTMTreeSearchScore.cpp:13:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
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:309:16: warning: unused variable 'ScoreOffset' [-Wunused-variable]
                unsigned int ScoreOffset;
                             ^
PTMTreeSearchScore.cpp:193:9: warning: unused variable 'fMaxIntens' [-Wunused-variable]
                float fMaxIntens = 0;
                      ^
PTMTreeSearchScore.cpp:195:8: warning: unused variable 'active' [-Wunused-variable]
                bool active;
                     ^
PTMTreeSearchScore.cpp: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;
              ^
40 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c base64.cpp -o base64.o
base64.cpp:11:28: warning: unused variable 'b64_pad' [-Wunused-const-variable]
static const unsigned char b64_pad = '=';
                           ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c dataLoader.cpp -o dataLoader.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c loadmspectrum.cpp -o loadmspectrum.o
In file included from loadmspectrum.cpp:142:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c masscalc.cpp -o masscalc.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c mbiomlreport.cpp -o mbiomlreport.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c mplugin.cpp -o mplugin.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c mprocess.cpp -o mprocess.o
In file included from mprocess.cpp:157:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
mprocess.cpp:440:7: warning: unused variable 'bC' [-Wunused-variable]
        bool bC = false;
             ^
mprocess.cpp:2476:9: warning: unused variable 'tLast' [-Wunused-variable]
        size_t tLast = 0;
               ^
mprocess.cpp:2472:9: warning: unused variable 'c' [-Wunused-variable]
        size_t c = 0;
               ^
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:4843:14: warning: unused variable 'crc' [-Wunused-variable]
    uint64_t crc = INITIALCRC, part = 0;
             ^
40 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c mrefine.cpp -o mrefine.o
In file included from mrefine.cpp:137:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
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;
               ^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
mreport.cpp:655:74: warning: array subscript is of type 'char' [-Wchar-subscripts]
                sprintf(pLine,"\t<aa type=\"%c\" mass=\"%.6lf\" />\n",cAa,_p.m_pdAaMass[cAa]);
                                                                                       ^˜˜˜
mreport.cpp:646:9: warning: unused variable 'a' [-Wunused-variable]
        size_t a = 0;
               ^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c mscore.cpp -o mscore.o
In file included from mscore.cpp:153:
In file included from ./mspectrum.h:142:
./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[']'];
                                           ^˜˜˜
50 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
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:587:10: warning: unused variable 'pfScore' [-Wunused-variable]
  float *pfScore = m_pSeqUtilFrag->m_pfBScore;
         ^
mscore_hrk.cpp:588:10: warning: unused variable 'pfScorePlus' [-Wunused-variable]
  float *pfScorePlus = m_pSeqUtilFrag->m_pfYScore;
         ^
mscore_hrk.cpp: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: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:736:10: warning: unused variable 'pfScore' [-Wunused-variable]
  float *pfScore = m_pSeqUtilFrag->m_pfYScore;
         ^
mscore_hrk.cpp:760:8: warning: unused variable 'lType' [-Wunused-variable]
  long lType = 0;
       ^
mscore_hrk.cpp:761:10: warning: unused variable 'b' [-Wunused-variable]
  size_t b = 0;
         ^
mscore_hrk.cpp:758:17: warning: unused variable 'a' [-Wunused-variable]
  unsigned long a = 0;
                ^
mscore_hrk.cpp:759:17: warning: unused variable 'lCount' [-Wunused-variable]
  unsigned long lCount = 0;
                ^
32 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
mscore_k.cpp:379:15: warning: unused variable 'lCount' [-Wunused-variable]
unsigned long lCount = 0;
              ^
mscore_k.cpp:381:8: warning: unused variable 'b' [-Wunused-variable]
size_t b = 0;
       ^
mscore_k.cpp:378:15: warning: unused variable 'a' [-Wunused-variable]
unsigned long a = 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:638:8: warning: unused variable 'dZ' [-Wunused-variable]
double dZ = (double)_c;
       ^
mscore_k.cpp:631:7: warning: unused variable 'fSub' [-Wunused-variable]
float fSub = 0.0;
      ^
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;
      ^
33 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
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:583:7: warning: unused variable 'lType' [-Wunused-variable]
        long lType = 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;
                      ^
7 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c msequencecollection.cpp -o msequencecollection.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c msequenceserver.cpp -o msequenceserver.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c msequtilities.cpp -o msequtilities.o
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: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'];
                                                          ^˜˜˜
274 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c mspectrumcondition.cpp -o mspectrumcondition.o
In file included from mspectrumcondition.cpp:154:
In file included from ./mspectrum.h:142:
./mhistogram.h:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c stdafx.cpp -o stdafx.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c tandem.cpp -o tandem.o
In file included from tandem.cpp:143:
In file included from ./tandem.h:15:
In file included from ./mspectrum.h:142:
./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:277:12: warning: unused variable 'tCount' [-Wunused-variable]
    size_t tCount = pProcess[0]->m_vSpectra.size();
           ^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -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:446:7: warning: unused variable 'lZeros' [-Wunused-variable]
                int lZeros = m_lHigh - a - 1;
                    ^
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
installing to /Users/biocbuild/bbs-2.14-bioc/meat/rTANDEM.Rcheck/rTANDEM/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rTANDEM)

rTANDEM.Rcheck/rTANDEM-Ex.timings:

nameusersystemelapsed
accessors0.8970.0340.931
converters0.0010.0010.002
parameters0.0280.0010.029
rTANDEM-package0.6490.0590.708
rTResult-class0.0040.0010.004
tandem0.5380.0450.583
visualizers0.2260.0020.227