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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL DIAlignR
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘DIAlignR’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ChromatogramPeak.cpp -o ChromatogramPeak.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c DPosition.cpp -o DPosition.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c MSChromatogram.cpp -o MSChromatogram.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c PeakIntegrator.cpp -o PeakIntegrator.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Rmain.cpp -o Rmain.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c affinealignment.cpp -o affinealignment.o
affinealignment.cpp: In function ‘void DIAlign::AffineAlignment::getAffineAlignedIndices(DIAlign::AffineAlignObj&, int)’:
affinealignment.cpp:260:11: warning: enumeration value ‘SS’ not handled in switch [-Wswitch]
     switch(TracebackPointer){
           ^
affinealignment.cpp: In function ‘double DIAlign::AffineAlignment::getOlapAffineAlignStartIndices(double*, double*, double*, int, int, int&, int&, DIAlign::Traceback::tbJump&)’:
affinealignment.cpp:483:16: warning: ‘MaxColIndex’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   OlapStartCol = MaxColIndex;
   ~~~~~~~~~~~~~^~~~~~~~~~~~~
affinealignment.cpp:482:16: warning: ‘MaxRowIndex’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   OlapStartRow = MaxRowIndex;
   ~~~~~~~~~~~~~^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c affinealignobj.cpp -o affinealignobj.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c alignment.cpp -o alignment.o
alignment.cpp: In function ‘void DIAlign::Alignment::getAlignedIndices(DIAlign::AlignObj&)’:
alignment.cpp:194:11: warning: enumeration value ‘SS’ not handled in switch [-Wswitch]
     switch(TracebackPointer){
           ^
alignment.cpp:194:11: warning: enumeration value ‘DA’ not handled in switch [-Wswitch]
alignment.cpp:194:11: warning: enumeration value ‘DB’ not handled in switch [-Wswitch]
alignment.cpp:194:11: warning: enumeration value ‘TA’ not handled in switch [-Wswitch]
alignment.cpp:194:11: warning: enumeration value ‘TB’ not handled in switch [-Wswitch]
alignment.cpp:194:11: warning: enumeration value ‘LA’ not handled in switch [-Wswitch]
alignment.cpp:194:11: warning: enumeration value ‘LB’ not handled in switch [-Wswitch]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c chromSimMatrix.cpp -o chromSimMatrix.o
chromSimMatrix.cpp: In function ‘std::vector<double> DIAlign::SimilarityMatrix::perSampleEucLenVecOfVec(const std::vector<std::vector<double> >&)’:
chromSimMatrix.cpp:32:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 0; i < mag.size(); i++){
                   ~~^~~~~~~~~~~~
chromSimMatrix.cpp: In function ‘std::vector<double> DIAlign::SimilarityMatrix::perSampleSqrSumVecOfVec(const std::vector<std::vector<double> >&)’:
chromSimMatrix.cpp:45:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 0; i < mag.size(); i++){
                   ~~^~~~~~~~~~~~
chromSimMatrix.cpp: In function ‘std::vector<double> DIAlign::SimilarityMatrix::perSampleMeanVecOfVec(const std::vector<std::vector<double> >&)’:
chromSimMatrix.cpp:57:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 0; i < mean.size(); i++){
                   ~~^~~~~~~~~~~~~
chromSimMatrix.cpp: In function ‘std::vector<double> DIAlign::SimilarityMatrix::perSampleSumVecOfVec(const std::vector<std::vector<double> >&)’:
chromSimMatrix.cpp:70:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 0; i < sum.size(); i++){
                   ~~^~~~~~~~~~~~
chromSimMatrix.cpp: In function ‘DIAlign::SimMatrix DIAlign::SimilarityMatrix::getSimilarityMatrix(const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, std::__cxx11::string, std::__cxx11::string, double, double)’:
chromSimMatrix.cpp:368:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0; i < MASK.size(); i++){
                    ~~^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c constrainMat.cpp -o constrainMat.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c gapPenalty.cpp -o gapPenalty.o
gapPenalty.cpp: In function ‘double DIAlign::getGapPenalty(const DIAlign::SimMatrix&, double, std::__cxx11::string)’:
gapPenalty.cpp:26:10: warning: ‘gapPenalty’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   return gapPenalty;
          ^~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c integrateArea.cpp -o integrateArea.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c interface.cpp -o interface.o
interface.cpp: In function ‘void DIAlign::printVecOfVec(Rcpp::List)’:
interface.cpp:17:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int j = 0; j < VecOfVec.size(); j++){
                  ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c run_alignment.cpp -o run_alignment.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c simpleFcn.cpp -o simpleFcn.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
utils.cpp: In function ‘double DIAlign::Utils::getQuantile(std::vector<double>, double)’:
utils.cpp:48:9: warning: unused variable ‘idx’ [-Wunused-variable]
     int idx = n*(1-p);
         ^~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o DIAlignR.so ChromatogramPeak.o DPosition.o MSChromatogram.o PeakIntegrator.o RcppExports.o Rmain.o affinealignment.o affinealignobj.o alignment.o chromSimMatrix.o constrainMat.o gapPenalty.o integrateArea.o interface.o run_alignment.o simpleFcn.o utils.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-DIAlignR/00new/DIAlignR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DIAlignR)