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INSTALL report for DIAlignR on tokay2

This page was generated on 2020-10-17 11:56:27 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE DIAlignR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 468/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DIAlignR 1.0.5
Shubham Gupta
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/DIAlignR
Branch: RELEASE_3_11
Last Commit: 4f8a0db
Last Changed Date: 2020-05-07 15:09:23 -0400 (Thu, 07 May 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DIAlignR
Version: 1.0.5
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/DIAlignR_1.0.5.tar.gz && rm -rf DIAlignR.buildbin-libdir && mkdir DIAlignR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DIAlignR.buildbin-libdir DIAlignR_1.0.5.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL DIAlignR_1.0.5.zip && rm DIAlignR_1.0.5.tar.gz DIAlignR_1.0.5.zip
StartedAt: 2020-10-16 18:04:15 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 18:07:23 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 188.2 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/DIAlignR_1.0.5.tar.gz && rm -rf DIAlignR.buildbin-libdir && mkdir DIAlignR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DIAlignR.buildbin-libdir DIAlignR_1.0.5.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL DIAlignR_1.0.5.zip && rm DIAlignR_1.0.5.tar.gz DIAlignR_1.0.5.zip
###
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##############################################################################


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install for i386

* installing *source* package 'DIAlignR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c ChromatogramPeak.cpp -o ChromatogramPeak.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c DPosition.cpp -o DPosition.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c MSChromatogram.cpp -o MSChromatogram.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c PeakIntegrator.cpp -o PeakIntegrator.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Rmain.cpp -o Rmain.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -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;
   ~~~~~~~~~~~~~^~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c affinealignobj.cpp -o affinealignobj.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -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]
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -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 of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i = 0; i < MASK.size(); i++){
                    ~~^~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c constrainMat.cpp -o constrainMat.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -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;
          ^~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c integrateArea.cpp -o integrateArea.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c interface.cpp -o interface.o
interface.cpp: In function 'void DIAlign::printVecOfVec(Rcpp::List)':
interface.cpp:17:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int j = 0; j < VecOfVec.size(); j++){
                  ~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c run_alignment.cpp -o run_alignment.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c simpleFcn.cpp -o simpleFcn.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -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);
         ^~~
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o DIAlignR.dll tmp.def 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 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/DIAlignR.buildbin-libdir/00LOCK-DIAlignR/00new/DIAlignR/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DIAlignR'
    finding HTML links ... done
    AffineAlignObj-class                    html  
    AffineAlignObjLight-class               html  
    AffineAlignObjMedium-class              html  
    AlignObj-class                          html  
    DIAlignR                                html  
    XIC_QFNNTDIVLLEDFQK_3_DIAlignR          html  
    alignChromatogramsCpp                   html  
    alignTargetedRuns                       html  
    analytesFromFeatures                    html  
    areaIntegrator                          html  
    as.list-AffineAlignObj-method           html  
    as.list-AffineAlignObjLight-method      html  
    as.list-AffineAlignObjMedium-method     html  
    as.list-AlignObj-method                 html  
    calculateIntensity                      html  
    chromatogramIdAsInteger                 html  
    constrainSimCpp                         html  
    doAffineAlignmentCpp                    html  
    doAlignmentCpp                          html  
    extractXIC_group                        html  
    fetchAnalytesInfo                       html  
    fetchFeaturesFromRun                    html  
    fetchPrecursorsInfo                     html  
    filenamesFromMZML                       html  
    filenamesFromOSW                        html  
    getAlignObj                             html  
    getAlignObjs                            html  
    getAlignedFigs                          html  
    getAlignedIndices                       html  
    getAnalytesQuery                        html  
    getBaseGapPenaltyCpp                    html  
    getChromSimMatCpp                       html  
    getChromatogramIndices                  html  
    getFeatures                             html  
    getFeaturesQuery                        html  
    getGlobalAlignMaskCpp                   html  
    getGlobalAlignment                      html  
    getGlobalFits                           html  
    getLOESSfit                             html  
    getLinearfit                            html  
    getMZMLpointers                         html  
    getMappedRT                             html  
    getMultipeptide                         html  
    getOswAnalytes                          html  
    getOswFiles                             html  
    getPrecursorByID                        html  
    getPrecursors                           html  
    getPrecursorsQuery                      html  
    getPrecursorsQueryID                    html  
    getQuery                                html  
    getRSE                                  html  
    getRefRun                               html  
    getRunNames                             html  
    getSeqSimMatCpp                         html  
    getXICs                                 html  
    getXICs4AlignObj                        html  
    mapIdxToTime                            html  
    mapPrecursorToChromIndices              html  
    mappedRTfromAlignObj                    html  
    mergeOswAnalytes_ChromHeader            html  
    multipeptide_DIAlignR                   html  
    oswFiles_DIAlignR                       html  
    pickNearestFeature                      html  
    plotAlignedAnalytes                     html  
    plotAlignmentPath                       html  
    plotAnalyteXICs                         html  
    plotSingleAlignedChrom                  html  
    plotXICgroup                            html  
    readChromatogramHeader                  html  
    setAlignmentRank                        html  
    smoothSingleXIC                         html  
    smoothXICs                              html  
    trimXICs                                html  
    updateFileInfo                          html  
    writeTables                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'DIAlignR' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c ChromatogramPeak.cpp -o ChromatogramPeak.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c DPosition.cpp -o DPosition.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c MSChromatogram.cpp -o MSChromatogram.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c PeakIntegrator.cpp -o PeakIntegrator.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Rmain.cpp -o Rmain.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -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;
   ~~~~~~~~~~~~~^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c affinealignobj.cpp -o affinealignobj.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -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]
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -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 of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
     for(int i = 0; i < MASK.size(); i++){
                    ~~^~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c constrainMat.cpp -o constrainMat.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -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;
          ^~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c integrateArea.cpp -o integrateArea.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c interface.cpp -o interface.o
interface.cpp: In function 'void DIAlign::printVecOfVec(Rcpp::List)':
interface.cpp:17:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   for(int j = 0; j < VecOfVec.size(); j++){
                  ~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c run_alignment.cpp -o run_alignment.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c simpleFcn.cpp -o simpleFcn.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -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);
         ^~~
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o DIAlignR.dll tmp.def 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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/DIAlignR.buildbin-libdir/DIAlignR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DIAlignR' as DIAlignR_1.0.5.zip
* DONE (DIAlignR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'DIAlignR' successfully unpacked and MD5 sums checked