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) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
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 468/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DIAlignR 1.0.5 Shubham Gupta
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| 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 |
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### Running command:
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### 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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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