rTANDEM 1.16.0
Frederic Fournier
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/rTANDEM | | Branch: RELEASE_3_5 | | Last Commit: 19152fb | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | [ OK ] | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD INSTALL rTANDEM
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* installing to library ‘/home/biocbuild/bbs-3.5-bioc/R/library’
* 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/R/library/rTANDEM/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘rTANDEM.Rnw’
** testing if installed package can be loaded
* DONE (rTANDEM)