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BioC 3.5: CHECK report for rTANDEM on malbec2

This page was generated on 2017-08-16 13:14:50 -0400 (Wed, 16 Aug 2017).

Package 1157/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rTANDEM 1.16.0
Frederic Fournier
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/rTANDEM
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rTANDEM
Version: 1.16.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings rTANDEM_1.16.0.tar.gz
StartedAt: 2017-08-16 02:02:41 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:05:01 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 140.2 seconds
RetCode: 0
Status:  OK 
CheckDir: rTANDEM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings rTANDEM_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/rTANDEM.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.16.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 16.4Mb
  sub-directories of 1Mb or more:
    extdata   3.2Mb
    libs     12.9Mb
* 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GetParamFromXML: no visible global function definition for
  ‘xmlTreeParse’
GetParamFromXML: no visible global function definition for ‘xmlRoot’
GetParamFromXML: no visible global function definition for
  ‘xmlChildren’
GetParamFromXML: no visible global function definition for ‘xmlName’
GetParamFromXML: no visible global function definition for ‘xmlAttrs’
GetParamFromXML: no visible global function definition for ‘xmlValue’
GetPeptides: no visible global function definition for ‘setnames’
GetProteins: no visible global function definition for ‘setkey’
GetResultsFromXML: no visible global function definition for ‘new’
GetResultsFromXML: no visible global function definition for
  ‘data.table’
GetResultsFromXML : protein: no visible global function definition for
  ‘data.table’
GetResultsFromXML : protein: no visible global function definition for
  ‘rbindlist’
GetResultsFromXML : protein: no visible global function definition for
  ‘set’
GetResultsFromXML : file: no visible global function definition for
  ‘set’
GetResultsFromXML : domain: no visible global function definition for
  ‘set’
GetResultsFromXML : domain: no visible global function definition for
  ‘data.table’
GetResultsFromXML : domain: no visible global function definition for
  ‘rbindlist’
GetResultsFromXML : aa: no visible global function definition for
  ‘data.table’
GetResultsFromXML : aa: no visible global function definition for
  ‘rbindlist’
GetResultsFromXML : aa: no visible global function definition for ‘set’
GetResultsFromXML : trace: no visible global function definition for
  ‘data.table’
GetResultsFromXML : trace: no visible global function definition for
  ‘rbindlist’
GetResultsFromXML : trace: no visible global function definition for
  ‘xmlChildren’
GetResultsFromXML : trace: no visible global function definition for
  ‘xmlGetAttr’
GetResultsFromXML : trace: no visible global function definition for
  ‘xmlValue’
GetResultsFromXML : trace: no visible global function definition for
  ‘set’
GetResultsFromXML : trace: no visible global function definition for
  ‘xmlAttrs’
GetResultsFromXML : note: no visible global function definition for
  ‘xmlAttrs’
GetResultsFromXML : note: no visible global function definition for
  ‘xmlValue’
GetResultsFromXML : note: no visible global function definition for
  ‘set’
GetResultsFromXML: no visible global function definition for
  ‘xmlEventParse’
GetResultsFromXML: no visible global function definition for ‘setkey’
GetResultsFromXML: no visible global function definition for ‘set’
GetTaxoFromXML: no visible global function definition for
  ‘xmlTreeParse’
GetTaxoFromXML: no visible global function definition for ‘getNodeSet’
GetTaxoFromXML: no visible global function definition for ‘xmlRoot’
GetTaxoFromXML: no visible global function definition for ‘xmlChildren’
GetTaxoFromXML: no visible global function definition for ‘xmlName’
GetTaxoFromXML: no visible global function definition for ‘xmlAttrs’
WriteParamToXML: no visible global function definition for ‘xmlNode’
WriteParamToXML: no visible global function definition for
  ‘addChildren’
WriteParamToXML: no visible global function definition for ‘saveXML’
WriteTaxoToXML: no visible global function definition for ‘xmlNode’
WriteTaxoToXML: no visible global function definition for ‘addChildren’
WriteTaxoToXML: no visible global function definition for ‘saveXML’
getParamFromXML: no visible global function definition for
  ‘xmlTreeParse’
getParamFromXML: no visible global function definition for ‘xmlRoot’
getParamFromXML: no visible global function definition for
  ‘xmlChildren’
getParamFromXML: no visible global function definition for ‘xmlName’
getParamFromXML: no visible global function definition for ‘xmlAttrs’
getParamFromXML: no visible global function definition for ‘xmlValue’
getPeptides: no visible global function definition for ‘setnames’
getProteins: no visible global function definition for ‘setkey’
getResultsFromXML: no visible global function definition for ‘new’
getResultsFromXML: no visible global function definition for
  ‘data.table’
getResultsFromXML : protein: no visible global function definition for
  ‘data.table’
getResultsFromXML : protein: no visible global function definition for
  ‘rbindlist’
getResultsFromXML : protein: no visible global function definition for
  ‘set’
getResultsFromXML : file: no visible global function definition for
  ‘set’
getResultsFromXML : domain: no visible global function definition for
  ‘set’
getResultsFromXML : domain: no visible global function definition for
  ‘data.table’
getResultsFromXML : domain: no visible global function definition for
  ‘rbindlist’
getResultsFromXML : aa: no visible global function definition for
  ‘data.table’
getResultsFromXML : aa: no visible global function definition for
  ‘rbindlist’
getResultsFromXML : aa: no visible global function definition for ‘set’
getResultsFromXML : trace: no visible global function definition for
  ‘data.table’
getResultsFromXML : trace: no visible global function definition for
  ‘rbindlist’
getResultsFromXML : trace: no visible global function definition for
  ‘xmlChildren’
getResultsFromXML : trace: no visible global function definition for
  ‘xmlGetAttr’
getResultsFromXML : trace: no visible global function definition for
  ‘xmlValue’
getResultsFromXML : trace: no visible global function definition for
  ‘set’
getResultsFromXML : trace: no visible global function definition for
  ‘xmlAttrs’
getResultsFromXML : note: no visible global function definition for
  ‘xmlAttrs’
getResultsFromXML : note: no visible global function definition for
  ‘xmlValue’
getResultsFromXML : note: no visible global function definition for
  ‘set’
getResultsFromXML: no visible global function definition for
  ‘xmlEventParse’
getResultsFromXML: no visible global function definition for ‘setkey’
getResultsFromXML: no visible global function definition for ‘set’
getTaxoFromXML: no visible global function definition for
  ‘xmlTreeParse’
getTaxoFromXML: no visible global function definition for ‘getNodeSet’
getTaxoFromXML: no visible global function definition for ‘xmlRoot’
getTaxoFromXML: no visible global function definition for ‘xmlChildren’
getTaxoFromXML: no visible global function definition for ‘xmlName’
getTaxoFromXML: no visible global function definition for ‘xmlAttrs’
ms2.plot: no visible global function definition for ‘is’
ms2.plot: no visible global function definition for ‘plot’
writeParamToXML: no visible global function definition for ‘xmlNode’
writeParamToXML: no visible global function definition for
  ‘addChildren’
writeParamToXML: no visible global function definition for ‘saveXML’
writeTaxoToXML: no visible global function definition for ‘xmlNode’
writeTaxoToXML: no visible global function definition for ‘addChildren’
writeTaxoToXML: no visible global function definition for ‘saveXML’
Undefined global functions or variables:
  addChildren data.table getNodeSet is new plot rbindlist saveXML set
  setkey setnames xmlAttrs xmlChildren xmlEventParse xmlGetAttr xmlName
  xmlNode xmlRoot xmlTreeParse xmlValue
Consider adding
  importFrom("graphics", "plot")
  importFrom("methods", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘rTANDEM/libs/rTANDEM.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘mreport.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘mreport.o’
File ‘rTANDEM/libs/rTANDEM.so’:
  Found non-API call to R: ‘R_CStackLimit’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/rTANDEM.Rcheck/00check.log’
for details.


rTANDEM.Rcheck/00install.out:

* installing *source* package ‘rTANDEM’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c PTMTreeSearch.cpp -o PTMTreeSearch.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from PTMTreeSearch.h:16,
                 from PTMTreeSearch.cpp:14:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
PTMTreeSearch.cpp: In member function ‘virtual bool PTMTreeSearch::refine()’:
PTMTreeSearch.cpp:304:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < m_pProcess->m_vSpectra[a].m_vMI.size(); ++i){
                   ^
PTMTreeSearch.cpp:308:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 1; i < spectraIntTMP.size(); ++i){
                   ^
PTMTreeSearch.cpp:382:12: warning: unused variable ‘dMaxExpect’ [-Wunused-variable]
     double dMaxExpect = atof(strValue.c_str());
            ^
PTMTreeSearch.cpp:402:67: warning: array subscript has type ‘char’ [-Wchar-subscripts]
    for (unsigned int k = 1; k < m_vmodModificationsDB[itAa->m_cRes].size(); k++){
                                                                   ^
PTMTreeSearch.cpp:403:34: warning: array subscript has type ‘char’ [-Wchar-subscripts]
      if (floor((mods[itAa->m_cRes][k])*10000) == iModSize){
                                  ^
PTMTreeSearch.cpp:405:37: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   m_vmodModificationsDB[itAa->m_cRes][k].m_uiCount++;
                                     ^
PTMTreeSearch.cpp:406:41: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   if (m_vmodModificationsDB[itAa->m_cRes][k].m_dTarget < itAa->m_fPval-1.0)
                                         ^
PTMTreeSearch.cpp:407:39: warning: array subscript has type ‘char’ [-Wchar-subscripts]
     m_vmodModificationsDB[itAa->m_cRes][k].m_dTarget = itAa->m_fPval-1.0;
                                       ^
PTMTreeSearch.cpp:408:41: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   if (m_vmodModificationsDB[itAa->m_cRes][k].m_dTargetEval > expect)
                                         ^
PTMTreeSearch.cpp:409:39: warning: array subscript has type ‘char’ [-Wchar-subscripts]
     m_vmodModificationsDB[itAa->m_cRes][k].m_dTargetEval = expect;
                                       ^
PTMTreeSearch.cpp:585:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (modCnt > noptmhitlimit){
              ^
PTMTreeSearch.cpp:54:10: warning: unused variable ‘tActiveNow’ [-Wunused-variable]
   size_t tActiveNow = 0;
          ^
PTMTreeSearch.cpp:66:10: warning: variable ‘dPTMMinEval’ set but not used [-Wunused-but-set-variable]
   double dPTMMinEval;
          ^
PTMTreeSearch.cpp:380:10: warning: unused variable ‘dMaxExpect’ [-Wunused-variable]
   double dMaxExpect = 0.1;
          ^
PTMTreeSearch.cpp: In member function ‘bool PTMTreeSearch::openUniprotPTMs(const char*, std::vector<Modification>*)’:
PTMTreeSearch.cpp:751:31: warning: array subscript has type ‘char’ [-Wchar-subscripts]
    m_vmodModificationsDB[resid].push_back(mod);
                               ^
PTMTreeSearch.cpp:676:16: warning: variable ‘m_uiId’ set but not used [-Wunused-but-set-variable]
   unsigned int m_uiId;  //unique id of the modification
                ^
PTMTreeSearch.cpp: In member function ‘virtual void SAXModsHandler::endElement(const XML_Char*)’:
PTMTreeSearch.cpp:875:29: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  m_vmodModificationsDB[resid].push_back(mod);
                             ^
PTMTreeSearch.cpp: In member function ‘virtual void SAXResidHandler::endElement(const XML_Char*)’:
PTMTreeSearch.cpp:1003:58: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       while (pos = m_strResidues.find(',')>m_strResidues.npos){
                                                          ^
PTMTreeSearch.cpp:1006:58: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       while (pos = m_strResidues.find(' ')>m_strResidues.npos){
                                                          ^
PTMTreeSearch.cpp:1018:29: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  m_vmodModificationsDB[resid].push_back(mod);
                             ^
PTMTreeSearch.cpp: In member function ‘virtual void SAXUnimodHandler::endElement(const XML_Char*)’:
PTMTreeSearch.cpp:1170:34: warning: array subscript has type ‘char’ [-Wchar-subscripts]
       m_vmodModificationsDB[resid].push_back(mod);
                                  ^
PTMTreeSearch.cpp:1156:10: warning: unused variable ‘pos’ [-Wunused-variable]
   size_t pos = 0;
          ^
PTMTreeSearch.cpp: In member function ‘bool PTMTreeSearch::openUniprotPTMs(const char*, std::vector<Modification>*)’:
PTMTreeSearch.cpp:744:31: warning: ‘m_dAveMass’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    mod.m_dAveMass = m_dAveMass;
                               ^
PTMTreeSearch.cpp:745:33: warning: ‘m_dMonoMass’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    mod.m_dMonoMass = m_dMonoMass;
                                 ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c PTMTreeSearchScore.cpp -o PTMTreeSearchScore.o
PTMTreeSearchScore.cpp:1264:1: warning: "/*" within comment [-Wcomment]
 /*
 ^
PTMTreeSearchScore.cpp:1366:1: warning: "/*" within comment [-Wcomment]
 /*
 ^
In file included from mspectrum.h:142:0,
                 from PTMTreeSearchScore.cpp:13:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
PTMTreeSearchScore.cpp: In member function ‘virtual float PTMTreeSearchScore::score(size_t)’:
PTMTreeSearchScore.cpp:369:35: warning: array subscript has type ‘char’ [-Wchar-subscripts]
    dPTM = m_pdMods[m_pSeq[uiLevel]][uiModIt];
                                   ^
PTMTreeSearchScore.cpp:373:47: warning: array subscript has type ‘char’ [-Wchar-subscripts]
     if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){ //this was the last modification, so delete this state
                                               ^
PTMTreeSearchScore.cpp:528:47: warning: array subscript has type ‘char’ [-Wchar-subscripts]
     if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){
                                               ^
PTMTreeSearchScore.cpp:568:47: warning: array subscript has type ‘char’ [-Wchar-subscripts]
     if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){
                                               ^
PTMTreeSearchScore.cpp:587:47: warning: array subscript has type ‘char’ [-Wchar-subscripts]
     if (uiModIt == m_uipModNum[m_pSeq[uiLevel]]){
                                               ^
PTMTreeSearchScore.cpp:193:9: warning: unused variable ‘fMaxIntens’ [-Wunused-variable]
   float fMaxIntens = 0;
         ^
PTMTreeSearchScore.cpp:195:8: warning: unused variable ‘active’ [-Wunused-variable]
   bool active;
        ^
PTMTreeSearchScore.cpp:309:16: warning: unused variable ‘ScoreOffset’ [-Wunused-variable]
   unsigned int ScoreOffset;
                ^
PTMTreeSearchScore.cpp:624:16: warning: unused variable ‘lValue’ [-Wunused-variable]
  unsigned long lValue = 0;
                ^
PTMTreeSearchScore.cpp: In member function ‘virtual bool PTMTreeSearchScore::get_aa(std::vector<maa>&, size_t, double&)’:
PTMTreeSearchScore.cpp:871:40: warning: array subscript has type ‘char’ [-Wchar-subscripts]
     aaValue.m_dMod = m_pdMods[m_pSeq[i]][m_pBestGoal->m_uipPTMMap[i]-1];
                                        ^
PTMTreeSearchScore.cpp: In member function ‘bool PTMTreeSearchScore::AnchorFixedModification()’:
PTMTreeSearchScore.cpp:903:52: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaMod[tC] + m_pSeqUtilFrag->m_pdAaFullMod[tC];
                                                    ^
PTMTreeSearchScore.cpp:903:88: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaMod[tC] + m_pSeqUtilFrag->m_pdAaFullMod[tC];
                                                                                        ^
PTMTreeSearchScore.cpp:905:56: warning: array subscript has type ‘char’ [-Wchar-subscripts]
    m_dFixResidues[a] += m_pSeqUtilFrag->m_pdAaPrompt[tC];
                                                        ^
PTMTreeSearchScore.cpp: In member function ‘bool PTMTreeSearchScore::add_dB(long unsigned int, long int)’:
PTMTreeSearchScore.cpp:1068:54: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   m_pfIntens[a] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
                                                      ^
PTMTreeSearchScore.cpp: In member function ‘bool PTMTreeSearchScore::add_dC(long unsigned int, long int)’:
PTMTreeSearchScore.cpp:1157:54: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   m_pfIntens[a] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
                                                      ^
PTMTreeSearchScore.cpp: In member function ‘bool PTMTreeSearchScore::add_dX(long unsigned int, long int)’:
PTMTreeSearchScore.cpp:1199:8: warning: unused variable ‘fSub’ [-Wunused-variable]
  float fSub = 0.0;
        ^
PTMTreeSearchScore.cpp: In member function ‘bool PTMTreeSearchScore::add_dY(long unsigned int, long int)’:
PTMTreeSearchScore.cpp:1305:59: warning: array subscript has type ‘char’ [-Wchar-subscripts]
     m_pfIntens[a-1] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                           ^
PTMTreeSearchScore.cpp:1314:58: warning: array subscript has type ‘char’ [-Wchar-subscripts]
    m_pfIntens[a-1] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                          ^
PTMTreeSearchScore.cpp:1271:8: warning: unused variable ‘fSub’ [-Wunused-variable]
  float fSub = 0.0;
        ^
PTMTreeSearchScore.cpp: In member function ‘bool PTMTreeSearchScore::add_dZ(long unsigned int, long int)’:
PTMTreeSearchScore.cpp:1405:57: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   m_pfIntens[a-1] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                         ^
PTMTreeSearchScore.cpp:1374:8: warning: unused variable ‘fSub’ [-Wunused-variable]
  float fSub = 0.0;
        ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c base64.cpp -o base64.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c dataLoader.cpp -o dataLoader.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c loadmspectrum.cpp -o loadmspectrum.o
In file included from mspectrum.h:142:0,
                 from loadmspectrum.cpp:142:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c masscalc.cpp -o masscalc.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c mbiomlreport.cpp -o mbiomlreport.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c mpam.cpp -o mpam.o
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mpam.cpp:137:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c mplugin.cpp -o mplugin.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c mpmods.cpp -o mpmods.o
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mpmods.cpp:137:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c mprocess.cpp -o mprocess.o
In file included from mspectrum.h:142:0,
                 from mprocess.cpp:157:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
mprocess.cpp: In member function ‘virtual bool mprocess::create_score(const msequence&, size_t, size_t, long int, bool)’:
mprocess.cpp:440:7: warning: unused variable ‘bC’ [-Wunused-variable]
  bool bC = false;
       ^
mprocess.cpp: In member function ‘bool mprocess::report_valid(double)’:
mprocess.cpp:2472:9: warning: unused variable ‘c’ [-Wunused-variable]
  size_t c = 0;
         ^
mprocess.cpp:2476:9: warning: unused variable ‘tLast’ [-Wunused-variable]
  size_t tLast = 0;
         ^
mprocess.cpp: In member function ‘bool mprocess::score_single(const msequence&)’:
mprocess.cpp:3390:46: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
       if(m_iCurrentRound == 1 && (m_bPermute && m_bCrcCheck || m_bPermuteHigh)) {
                                              ^
mprocess.cpp: In member function ‘bool mprocess::initialize_crc()’:
mprocess.cpp:4843:14: warning: unused variable ‘crc’ [-Wunused-variable]
     uint64_t crc = INITIALCRC, part = 0;
              ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c mrefine.cpp -o mrefine.o
In file included from mspectrum.h:142:0,
                 from mrefine.cpp:137:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
mrefine.cpp: In member function ‘virtual bool mrefine::refine()’:
mrefine.cpp:250:9: warning: unused variable ‘a’ [-Wunused-variable]
  size_t a = 0;
         ^
mrefine.cpp:251:9: warning: unused variable ‘tActiveNow’ [-Wunused-variable]
  size_t tActiveNow = 0;
         ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c mreport.cpp -o mreport.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxsaphandler.h:140,
                 from mreport.cpp:143:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
mreport.cpp: In member function ‘bool mreport::masses(msequtilities&)’:
mreport.cpp:655:78: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   sprintf(pLine,"\t<aa type=\"%c\" mass=\"%.6lf\" />\n",cAa,_p.m_pdAaMass[cAa]);
                                                                              ^
mreport.cpp:646:9: warning: unused variable ‘a’ [-Wunused-variable]
  size_t a = 0;
         ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c mscore.cpp -o mscore.o
In file included from mspectrum.h:142:0,
                 from mscore.cpp:153:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
mscore.cpp: In constructor ‘mscore::mscore()’:
mscore.cpp:200:19: warning: iteration 16u invokes undefined behavior [-Waggressive-loop-optimizations]
   m_plCount[a] = 0;
                   ^
mscore.cpp:199:10: note: containing loop
  while(a < 20) {
          ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c mscore_hrk.cpp -o mscore_hrk.o
In file included from mspectrum.h:142:0,
                 from mscore_hrk.cpp:24:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
mscore_hrk.cpp: In member function ‘virtual double mscore_hrk::dot(long unsigned int*)’:
mscore_hrk.cpp:305:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (itType != itEnd && iIon == itType->m_lM) {
                                 ^
mscore_hrk.cpp:314:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (itType != itBegin && iIon - 1 == itType[-1].m_lM) {
                                       ^
mscore_hrk.cpp:321:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (itGreater != itEnd && iIon + 1 == itGreater->m_lM) {
                                        ^
mscore_hrk.cpp: In member function ‘bool mscore_hrk::add_mi_hr(mspectrum&)’:
mscore_hrk.cpp:443:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(ii==tempLookup.size()-1) break;
            ^
mscore_hrk.cpp:352:7: warning: unused variable ‘iTotI’ [-Wunused-variable]
   int iTotI = 0;
       ^
mscore_hrk.cpp:371:7: warning: unused variable ‘peakCount’ [-Wunused-variable]
   int peakCount = 0;
       ^
mscore_hrk.cpp: In member function ‘double mscore_hrk::dot_hr(long unsigned int*)’:
mscore_hrk.cpp:491:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if(i==m_vmiType[m_lId].size()){
           ^
mscore_hrk.cpp: In member function ‘virtual bool mscore_hrk::add_A(long unsigned int, long int)’:
mscore_hrk.cpp:550:10: warning: unused variable ‘pfScore’ [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfAScore;
          ^
mscore_hrk.cpp: In member function ‘virtual bool mscore_hrk::add_B(long unsigned int, long int)’:
mscore_hrk.cpp:587:10: warning: unused variable ‘pfScore’ [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfBScore;
          ^
mscore_hrk.cpp:588:10: warning: unused variable ‘pfScorePlus’ [-Wunused-variable]
   float *pfScorePlus = m_pSeqUtilFrag->m_pfYScore;
          ^
mscore_hrk.cpp: In member function ‘virtual bool mscore_hrk::add_C(long unsigned int, long int)’:
mscore_hrk.cpp:622:10: warning: unused variable ‘pfScore’ [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfBScore;
          ^
mscore_hrk.cpp:623:10: warning: unused variable ‘pfScorePlus’ [-Wunused-variable]
   float *pfScorePlus = m_pSeqUtilFrag->m_pfYScore;
          ^
mscore_hrk.cpp: In member function ‘virtual bool mscore_hrk::add_X(long unsigned int, long int)’:
mscore_hrk.cpp:657:9: warning: unused variable ‘fSub’ [-Wunused-variable]
   float fSub = 0.0;
         ^
mscore_hrk.cpp:658:10: warning: unused variable ‘pfScore’ [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfXScore;
          ^
mscore_hrk.cpp: In member function ‘virtual bool mscore_hrk::add_Y(long unsigned int, long int)’:
mscore_hrk.cpp:691:9: warning: unused variable ‘fSub’ [-Wunused-variable]
   float fSub = 0.0;
         ^
mscore_hrk.cpp:692:10: warning: unused variable ‘pfScore’ [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfYScore;
          ^
mscore_hrk.cpp:693:10: warning: unused variable ‘pfScoreMinus’ [-Wunused-variable]
   float *pfScoreMinus = m_pSeqUtilFrag->m_pfBScore;
          ^
mscore_hrk.cpp: In member function ‘virtual bool mscore_hrk::add_Z(long unsigned int, long int)’:
mscore_hrk.cpp:735:9: warning: unused variable ‘fSub’ [-Wunused-variable]
   float fSub = 0.0;
         ^
mscore_hrk.cpp:736:10: warning: unused variable ‘pfScore’ [-Wunused-variable]
   float *pfScore = m_pSeqUtilFrag->m_pfYScore;
          ^
mscore_hrk.cpp:737:10: warning: unused variable ‘pfScoreMinus’ [-Wunused-variable]
   float *pfScoreMinus = m_pSeqUtilFrag->m_pfBScore;
          ^
mscore_hrk.cpp: In member function ‘virtual float mscore_hrk::ion_check(long unsigned int, size_t)’:
mscore_hrk.cpp:758:17: warning: unused variable ‘a’ [-Wunused-variable]
   unsigned long a = 0;
                 ^
mscore_hrk.cpp:759:17: warning: unused variable ‘lCount’ [-Wunused-variable]
   unsigned long lCount = 0;
                 ^
mscore_hrk.cpp:760:8: warning: unused variable ‘lType’ [-Wunused-variable]
   long lType = 0;
        ^
mscore_hrk.cpp:761:10: warning: unused variable ‘b’ [-Wunused-variable]
   size_t b = 0;
          ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c mscore_k.cpp -o mscore_k.o
mscore_k.cpp:677:1: warning: "/*" within comment [-Wcomment]
 /*
 ^
mscore_k.cpp:753:1: warning: "/*" within comment [-Wcomment]
 /*
 ^
In file included from mspectrum.h:142:0,
                 from mscore_k.cpp:24:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
mscore_k.cpp: In member function ‘virtual double mscore_k::dot(long unsigned int*)’:
mscore_k.cpp:344:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (itType != itEnd && iIon == itType->m_lM) {
                                     ^
mscore_k.cpp:355:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (itType != itBegin && iIon - 1 == itType[-1].m_lM) {
                                           ^
mscore_k.cpp:363:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (itGreater != itEnd && iIon + 1 == itGreater->m_lM) {
                                            ^
mscore_k.cpp: In member function ‘virtual float mscore_k::ion_check(long unsigned int, size_t)’:
mscore_k.cpp:378:15: warning: unused variable ‘a’ [-Wunused-variable]
 unsigned long a = 0;
               ^
mscore_k.cpp:379:15: warning: unused variable ‘lCount’ [-Wunused-variable]
 unsigned long lCount = 0;
               ^
mscore_k.cpp:380:6: warning: unused variable ‘lType’ [-Wunused-variable]
 long lType = 0;
      ^
mscore_k.cpp:381:8: warning: unused variable ‘b’ [-Wunused-variable]
 size_t b = 0;
        ^
mscore_k.cpp: In member function ‘virtual bool mscore_k::add_A(long unsigned int, long int)’:
mscore_k.cpp:466:14: warning: unused variable ‘dZ’ [-Wunused-variable]
 const double dZ = (double)_c;
              ^
mscore_k.cpp: In member function ‘virtual bool mscore_k::add_B(long unsigned int, long int)’:
mscore_k.cpp:529:54: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
                                                      ^
mscore_k.cpp:523:14: warning: unused variable ‘dZ’ [-Wunused-variable]
 const double dZ = (double)_c;
              ^
mscore_k.cpp: In member function ‘virtual bool mscore_k::add_C(long unsigned int, long int)’:
mscore_k.cpp:591:54: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
                                                      ^
mscore_k.cpp:584:8: warning: unused variable ‘dZ’ [-Wunused-variable]
 double dZ = (double)_c;
        ^
mscore_k.cpp: In member function ‘virtual bool mscore_k::add_X(long unsigned int, long int)’:
mscore_k.cpp:631:7: warning: unused variable ‘fSub’ [-Wunused-variable]
 float fSub = 0.0;
       ^
mscore_k.cpp:638:8: warning: unused variable ‘dZ’ [-Wunused-variable]
 double dZ = (double)_c;
        ^
mscore_k.cpp: In member function ‘virtual bool mscore_k::add_Y(long unsigned int, long int)’:
mscore_k.cpp:706:55: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                       ^
mscore_k.cpp:712:55: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                       ^
mscore_k.cpp:684:7: warning: unused variable ‘fSub’ [-Wunused-variable]
 float fSub = 0.0;
       ^
mscore_k.cpp:694:8: warning: unused variable ‘dZ’ [-Wunused-variable]
 double dZ = (double)_c;
        ^
mscore_k.cpp: In member function ‘virtual bool mscore_k::add_Z(long unsigned int, long int)’:
mscore_k.cpp:776:55: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                       ^
mscore_k.cpp:779:55: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                       ^
mscore_k.cpp:761:7: warning: unused variable ‘fSub’ [-Wunused-variable]
 float fSub = 0.0;
       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c mscore_tandem.cpp -o mscore_tandem.o
In file included from mspectrum.h:142:0,
                 from mscore_tandem.cpp:135:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
mscore_tandem.cpp: In member function ‘bool mscore_tandem::blur(std::vector<mi>&)’:
mscore_tandem.cpp:288:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(uType.m_lM == lValue + a) {
                   ^
mscore_tandem.cpp: In member function ‘virtual double mscore_tandem::dot(long unsigned int*)’:
mscore_tandem.cpp:358:8: warning: unused variable ‘fValue0’ [-Wunused-variable]
  float fValue0 = 0.0;
        ^
mscore_tandem.cpp:362:9: warning: unused variable ‘b’ [-Wunused-variable]
  size_t b = 0;
         ^
mscore_tandem.cpp: In member function ‘virtual float mscore_tandem::ion_check(long unsigned int, size_t)’:
mscore_tandem.cpp:581:16: warning: unused variable ‘a’ [-Wunused-variable]
  unsigned long a = 0;
                ^
mscore_tandem.cpp:582:16: warning: unused variable ‘lCount’ [-Wunused-variable]
  unsigned long lCount = 0;
                ^
mscore_tandem.cpp:583:7: warning: unused variable ‘lType’ [-Wunused-variable]
  long lType = 0;
       ^
mscore_tandem.cpp:584:9: warning: unused variable ‘b’ [-Wunused-variable]
  size_t b = 0;
         ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c msequencecollection.cpp -o msequencecollection.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c msequenceserver.cpp -o msequenceserver.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c msequtilities.cpp -o msequtilities.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c mspectrumcondition.cpp -o mspectrumcondition.o
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.cpp:154:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c mtermmods.cpp -o mtermmods.o
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mtermmods.cpp:137:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c mxxcleavage.cpp -o mxxcleavage.o
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mxxcleavage.cpp:137:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c saxbiomlhandler.cpp -o saxbiomlhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxbiomlhandler.h:140,
                 from saxbiomlhandler.cpp:140:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c saxgamlhandler.cpp -o saxgamlhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxgamlhandler.h:140,
                 from saxgamlhandler.cpp:139:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c saxhandler.cpp -o saxhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxhandler.cpp:132:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c saxmodhandler.cpp -o saxmodhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxmodhandler.h:140,
                 from saxmodhandler.cpp:140:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c saxmzdatahandler.cpp -o saxmzdatahandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxmzdatahandler.h:4,
                 from saxmzdatahandler.cpp:28:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c saxmzmlhandler.cpp -o saxmzmlhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxmzmlhandler.h:4,
                 from saxmzmlhandler.cpp:33:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c saxmzxmlhandler.cpp -o saxmzxmlhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxmzxmlhandler.h:4,
                 from saxmzxmlhandler.cpp:20:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c saxsaphandler.cpp -o saxsaphandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxsaphandler.h:140,
                 from saxsaphandler.cpp:140:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c saxtandeminputhandler.cpp -o saxtandeminputhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxtandeminputhandler.h:140,
                 from saxtandeminputhandler.cpp:139:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c saxtaxhandler.cpp -o saxtaxhandler.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxtaxhandler.h:140,
                 from saxtaxhandler.cpp:139:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c stdafx.cpp -o stdafx.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c tandem.cpp -o tandem.o
In file included from mspectrum.h:142:0,
                 from tandem.h:15,
                 from tandem.cpp:143:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
tandem.cpp: In function ‘SEXPREC* tandem(SEXP, SEXP, SEXP, SEXP, SEXP)’:
tandem.cpp:277:12: warning: unused variable ‘tCount’ [-Wunused-variable]
     size_t tCount = pProcess[0]->m_vSpectra.size();
            ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c xmlparameter.cpp -o xmlparameter.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxtandeminputhandler.h:140,
                 from xmlparameter.cpp:144:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c xmltaxonomy.cpp -o xmltaxonomy.o
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxtaxhandler.h:140,
                 from xmltaxonomy.cpp:160:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446:7: warning: unused variable ‘lZeros’ [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o rTANDEM.so PTMTreeSearch.o PTMTreeSearchScore.o base64.o dataLoader.o loadmspectrum.o masscalc.o mbiomlreport.o mpam.o mplugin.o mpmods.o mprocess.o mrefine.o mreport.o mscore.o mscore_hrk.o mscore_k.o mscore_tandem.o msequencecollection.o msequenceserver.o msequtilities.o mspectrumcondition.o mtermmods.o mxxcleavage.o saxbiomlhandler.o saxgamlhandler.o saxhandler.o saxmodhandler.o saxmzdatahandler.o saxmzmlhandler.o saxmzxmlhandler.o saxsaphandler.o saxtandeminputhandler.o saxtaxhandler.o stdafx.o tandem.o xmlparameter.o xmltaxonomy.o -lpthread -lexpat -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-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
accessors1.2640.0241.008
converters0.0000.0000.002
parameters0.0400.0000.039
rTANDEM-package0.4400.0040.446
rTResult-class0.0000.0000.002
tandem0.3960.0000.394
visualizers0.4760.0000.387