BioC 3.1: INSTALL report for rTANDEM on petty

Package: rTANDEM

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rTANDEM

StartedAt: 2015-10-08 18:05:14 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 18:08:07 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 173.2 seconds

RetCode: 0

Status:  OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rTANDEM
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library’
* installing *source* package ‘rTANDEM’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c PTMTreeSearch.cpp -o PTMTreeSearch.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from PTMTreeSearch.h:16,
                 from PTMTreeSearch.cpp:14:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
PTMTreeSearch.cpp: In member function ‘virtual bool PTMTreeSearch::refine()’:
PTMTreeSearch.cpp:304: warning: comparison between signed and unsigned integer expressions
PTMTreeSearch.cpp:308: warning: comparison between signed and unsigned integer expressions
PTMTreeSearch.cpp:382: warning: unused variable ‘dMaxExpect’
PTMTreeSearch.cpp:402: warning: array subscript has type ‘char’
PTMTreeSearch.cpp:403: warning: array subscript has type ‘char’
PTMTreeSearch.cpp:405: warning: array subscript has type ‘char’
PTMTreeSearch.cpp:406: warning: array subscript has type ‘char’
PTMTreeSearch.cpp:407: warning: array subscript has type ‘char’
PTMTreeSearch.cpp:408: warning: array subscript has type ‘char’
PTMTreeSearch.cpp:409: warning: array subscript has type ‘char’
PTMTreeSearch.cpp:585: warning: comparison between signed and unsigned integer expressions
PTMTreeSearch.cpp:54: warning: unused variable ‘tActiveNow’
PTMTreeSearch.cpp:380: warning: unused variable ‘dMaxExpect’
PTMTreeSearch.cpp: In member function ‘bool PTMTreeSearch::openUniprotPTMs(const char*, std::vector<Modification, std::allocator<Modification> >*)’:
PTMTreeSearch.cpp:751: warning: array subscript has type ‘char’
PTMTreeSearch.cpp: In member function ‘virtual void SAXResidHandler::endElement(const XML_Char*)’:
PTMTreeSearch.cpp:1003: warning: suggest parentheses around assignment used as truth value
PTMTreeSearch.cpp:1006: warning: suggest parentheses around assignment used as truth value
PTMTreeSearch.cpp: In member function ‘virtual void SAXUnimodHandler::endElement(const XML_Char*)’:
PTMTreeSearch.cpp:1156: warning: unused variable ‘pos’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c PTMTreeSearchScore.cpp -o PTMTreeSearchScore.o
PTMTreeSearchScore.cpp:1264:1: warning: "/*" within comment
PTMTreeSearchScore.cpp:1366:1: warning: "/*" within comment
In file included from mspectrum.h:142,
                 from PTMTreeSearchScore.cpp:13:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
PTMTreeSearchScore.cpp: In member function ‘virtual float PTMTreeSearchScore::score(size_t)’:
PTMTreeSearchScore.cpp:193: warning: unused variable ‘fMaxIntens’
PTMTreeSearchScore.cpp:195: warning: unused variable ‘active’
PTMTreeSearchScore.cpp:309: warning: unused variable ‘ScoreOffset’
PTMTreeSearchScore.cpp:624: warning: unused variable ‘lValue’
PTMTreeSearchScore.cpp: In member function ‘bool PTMTreeSearchScore::add_dX(long unsigned int, long int)’:
PTMTreeSearchScore.cpp:1199: warning: unused variable ‘fSub’
PTMTreeSearchScore.cpp: In member function ‘bool PTMTreeSearchScore::add_dY(long unsigned int, long int)’:
PTMTreeSearchScore.cpp:1271: warning: unused variable ‘fSub’
PTMTreeSearchScore.cpp: In member function ‘bool PTMTreeSearchScore::add_dZ(long unsigned int, long int)’:
PTMTreeSearchScore.cpp:1374: warning: unused variable ‘fSub’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c base64.cpp -o base64.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c dataLoader.cpp -o dataLoader.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c loadmspectrum.cpp -o loadmspectrum.o
In file included from mspectrum.h:142,
                 from loadmspectrum.cpp:142:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c masscalc.cpp -o masscalc.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c mbiomlreport.cpp -o mbiomlreport.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c mpam.cpp -o mpam.o
In file included from mspectrum.h:142,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mpam.cpp:137:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c mplugin.cpp -o mplugin.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c mpmods.cpp -o mpmods.o
In file included from mspectrum.h:142,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mpmods.cpp:137:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c mprocess.cpp -o mprocess.o
In file included from mspectrum.h:142,
                 from mprocess.cpp:157:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
mprocess.cpp: In member function ‘virtual bool mprocess::create_score(const msequence&, size_t, size_t, long int, bool)’:
mprocess.cpp:440: warning: unused variable ‘bC’
mprocess.cpp: In member function ‘bool mprocess::report_valid(double)’:
mprocess.cpp:2472: warning: unused variable ‘c’
mprocess.cpp:2476: warning: unused variable ‘tLast’
mprocess.cpp: In member function ‘bool mprocess::initialize_crc()’:
mprocess.cpp:4843: warning: unused variable ‘crc’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c mrefine.cpp -o mrefine.o
In file included from mspectrum.h:142,
                 from mrefine.cpp:137:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
mrefine.cpp: In member function ‘virtual bool mrefine::refine()’:
mrefine.cpp:250: warning: unused variable ‘a’
mrefine.cpp:251: warning: unused variable ‘tActiveNow’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c mreport.cpp -o mreport.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxsaphandler.h:140,
                 from mreport.cpp:143:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
mreport.cpp: In member function ‘bool mreport::masses(msequtilities&)’:
mreport.cpp:646: warning: unused variable ‘a’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c mscore.cpp -o mscore.o
In file included from mspectrum.h:142,
                 from mscore.cpp:153:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c mscore_hrk.cpp -o mscore_hrk.o
In file included from mspectrum.h:142,
                 from mscore_hrk.cpp:24:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
mscore_hrk.cpp: In member function ‘virtual double mscore_hrk::dot(long unsigned int*)’:
mscore_hrk.cpp:305: warning: comparison between signed and unsigned integer expressions
mscore_hrk.cpp:314: warning: comparison between signed and unsigned integer expressions
mscore_hrk.cpp:321: warning: comparison between signed and unsigned integer expressions
mscore_hrk.cpp: In member function ‘bool mscore_hrk::add_mi_hr(mspectrum&)’:
mscore_hrk.cpp:443: warning: comparison between signed and unsigned integer expressions
mscore_hrk.cpp:352: warning: unused variable ‘iTotI’
mscore_hrk.cpp:371: warning: unused variable ‘peakCount’
mscore_hrk.cpp: In member function ‘double mscore_hrk::dot_hr(long unsigned int*)’:
mscore_hrk.cpp:491: warning: comparison between signed and unsigned integer expressions
mscore_hrk.cpp: In member function ‘virtual bool mscore_hrk::add_A(long unsigned int, long int)’:
mscore_hrk.cpp:550: warning: unused variable ‘pfScore’
mscore_hrk.cpp: In member function ‘virtual bool mscore_hrk::add_B(long unsigned int, long int)’:
mscore_hrk.cpp:587: warning: unused variable ‘pfScore’
mscore_hrk.cpp:588: warning: unused variable ‘pfScorePlus’
mscore_hrk.cpp: In member function ‘virtual bool mscore_hrk::add_C(long unsigned int, long int)’:
mscore_hrk.cpp:622: warning: unused variable ‘pfScore’
mscore_hrk.cpp:623: warning: unused variable ‘pfScorePlus’
mscore_hrk.cpp: In member function ‘virtual bool mscore_hrk::add_X(long unsigned int, long int)’:
mscore_hrk.cpp:657: warning: unused variable ‘fSub’
mscore_hrk.cpp:658: warning: unused variable ‘pfScore’
mscore_hrk.cpp: In member function ‘virtual bool mscore_hrk::add_Y(long unsigned int, long int)’:
mscore_hrk.cpp:691: warning: unused variable ‘fSub’
mscore_hrk.cpp:692: warning: unused variable ‘pfScore’
mscore_hrk.cpp:693: warning: unused variable ‘pfScoreMinus’
mscore_hrk.cpp: In member function ‘virtual bool mscore_hrk::add_Z(long unsigned int, long int)’:
mscore_hrk.cpp:735: warning: unused variable ‘fSub’
mscore_hrk.cpp:736: warning: unused variable ‘pfScore’
mscore_hrk.cpp:737: warning: unused variable ‘pfScoreMinus’
mscore_hrk.cpp: In member function ‘virtual float mscore_hrk::ion_check(long unsigned int, size_t)’:
mscore_hrk.cpp:758: warning: unused variable ‘a’
mscore_hrk.cpp:759: warning: unused variable ‘lCount’
mscore_hrk.cpp:760: warning: unused variable ‘lType’
mscore_hrk.cpp:761: warning: unused variable ‘b’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c mscore_k.cpp -o mscore_k.o
mscore_k.cpp:677:1: warning: "/*" within comment
mscore_k.cpp:753:1: warning: "/*" within comment
In file included from mspectrum.h:142,
                 from mscore_k.cpp:24:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
mscore_k.cpp: In member function ‘virtual double mscore_k::dot(long unsigned int*)’:
mscore_k.cpp:344: warning: comparison between signed and unsigned integer expressions
mscore_k.cpp:355: warning: comparison between signed and unsigned integer expressions
mscore_k.cpp:363: warning: comparison between signed and unsigned integer expressions
mscore_k.cpp: In member function ‘virtual float mscore_k::ion_check(long unsigned int, size_t)’:
mscore_k.cpp:378: warning: unused variable ‘a’
mscore_k.cpp:379: warning: unused variable ‘lCount’
mscore_k.cpp:380: warning: unused variable ‘lType’
mscore_k.cpp:381: warning: unused variable ‘b’
mscore_k.cpp: In member function ‘virtual bool mscore_k::add_A(long unsigned int, long int)’:
mscore_k.cpp:466: warning: unused variable ‘dZ’
mscore_k.cpp: In member function ‘virtual bool mscore_k::add_B(long unsigned int, long int)’:
mscore_k.cpp:523: warning: unused variable ‘dZ’
mscore_k.cpp: In member function ‘virtual bool mscore_k::add_C(long unsigned int, long int)’:
mscore_k.cpp:584: warning: unused variable ‘dZ’
mscore_k.cpp: In member function ‘virtual bool mscore_k::add_X(long unsigned int, long int)’:
mscore_k.cpp:631: warning: unused variable ‘fSub’
mscore_k.cpp:638: warning: unused variable ‘dZ’
mscore_k.cpp: In member function ‘virtual bool mscore_k::add_Y(long unsigned int, long int)’:
mscore_k.cpp:684: warning: unused variable ‘fSub’
mscore_k.cpp:694: warning: unused variable ‘dZ’
mscore_k.cpp: In member function ‘virtual bool mscore_k::add_Z(long unsigned int, long int)’:
mscore_k.cpp:761: warning: unused variable ‘fSub’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c mscore_tandem.cpp -o mscore_tandem.o
In file included from mspectrum.h:142,
                 from mscore_tandem.cpp:135:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
mscore_tandem.cpp: In member function ‘bool mscore_tandem::blur(std::vector<mi, std::allocator<mi> >&)’:
mscore_tandem.cpp:288: warning: comparison between signed and unsigned integer expressions
mscore_tandem.cpp: In member function ‘virtual double mscore_tandem::dot(long unsigned int*)’:
mscore_tandem.cpp:358: warning: unused variable ‘fValue0’
mscore_tandem.cpp:362: warning: unused variable ‘b’
mscore_tandem.cpp: In member function ‘virtual float mscore_tandem::ion_check(long unsigned int, size_t)’:
mscore_tandem.cpp:581: warning: unused variable ‘a’
mscore_tandem.cpp:582: warning: unused variable ‘lCount’
mscore_tandem.cpp:583: warning: unused variable ‘lType’
mscore_tandem.cpp:584: warning: unused variable ‘b’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c msequencecollection.cpp -o msequencecollection.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c msequenceserver.cpp -o msequenceserver.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c msequtilities.cpp -o msequtilities.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c mspectrumcondition.cpp -o mspectrumcondition.o
In file included from mspectrum.h:142,
                 from mspectrumcondition.cpp:154:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c mtermmods.cpp -o mtermmods.o
In file included from mspectrum.h:142,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mtermmods.cpp:137:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c mxxcleavage.cpp -o mxxcleavage.o
In file included from mspectrum.h:142,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mxxcleavage.cpp:137:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c saxbiomlhandler.cpp -o saxbiomlhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxbiomlhandler.h:140,
                 from saxbiomlhandler.cpp:140:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c saxgamlhandler.cpp -o saxgamlhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxgamlhandler.h:140,
                 from saxgamlhandler.cpp:139:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c saxhandler.cpp -o saxhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxhandler.cpp:132:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c saxmodhandler.cpp -o saxmodhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxmodhandler.h:140,
                 from saxmodhandler.cpp:140:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c saxmzdatahandler.cpp -o saxmzdatahandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxmzdatahandler.h:4,
                 from saxmzdatahandler.cpp:28:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c saxmzmlhandler.cpp -o saxmzmlhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxmzmlhandler.h:4,
                 from saxmzmlhandler.cpp:33:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c saxmzxmlhandler.cpp -o saxmzxmlhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxmzxmlhandler.h:4,
                 from saxmzxmlhandler.cpp:20:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c saxsaphandler.cpp -o saxsaphandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxsaphandler.h:140,
                 from saxsaphandler.cpp:140:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c saxtandeminputhandler.cpp -o saxtandeminputhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxtandeminputhandler.h:140,
                 from saxtandeminputhandler.cpp:139:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c saxtaxhandler.cpp -o saxtaxhandler.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxtaxhandler.h:140,
                 from saxtaxhandler.cpp:139:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c stdafx.cpp -o stdafx.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c tandem.cpp -o tandem.o
In file included from mspectrum.h:142,
                 from tandem.h:15,
                 from tandem.cpp:143:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
tandem.cpp: In function ‘SEXPREC* tandem(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
tandem.cpp:277: warning: unused variable ‘tCount’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c xmlparameter.cpp -o xmlparameter.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxtandeminputhandler.h:140,
                 from xmlparameter.cpp:144:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c xmltaxonomy.cpp -o xmltaxonomy.o
In file included from mspectrum.h:142,
                 from saxhandler.h:137,
                 from saxtaxhandler.h:140,
                 from xmltaxonomy.cpp:160:
mhistogram.h: In member function ‘bool mhistogram::model()’:
mhistogram.h:446: warning: unused variable ‘lZeros’
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o rTANDEM.so PTMTreeSearch.o PTMTreeSearchScore.o base64.o dataLoader.o loadmspectrum.o masscalc.o mbiomlreport.o mpam.o mplugin.o mpmods.o mprocess.o mrefine.o mreport.o mscore.o mscore_hrk.o mscore_k.o mscore_tandem.o msequencecollection.o msequenceserver.o msequtilities.o mspectrumcondition.o mtermmods.o mxxcleavage.o saxbiomlhandler.o saxgamlhandler.o saxhandler.o saxmodhandler.o saxmzdatahandler.o saxmzmlhandler.o saxmzxmlhandler.o saxsaphandler.o saxtandeminputhandler.o saxtaxhandler.o stdafx.o tandem.o xmlparameter.o xmltaxonomy.o -lpthread -lexpat -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.2/Resources/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)