############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/kebabs_1.28.1.tar.gz && rm -rf kebabs.buildbin-libdir && mkdir kebabs.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=kebabs.buildbin-libdir kebabs_1.28.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL kebabs_1.28.1.zip && rm kebabs_1.28.1.tar.gz kebabs_1.28.1.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 8 1775k 8 159k 0 0 457k 0 0:00:03 --:--:-- 0:00:03 457k 75 1775k 75 1335k 0 0 985k 0 0:00:01 0:00:01 --:--:-- 985k 100 1775k 100 1775k 0 0 986k 0 0:00:01 0:00:01 --:--:-- 986k install for i386 * installing *source* package 'kebabs' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ByteStringVector.c -o ByteStringVector.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ExplicitRepC.cpp -o ExplicitRepC.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GappyPairC.cpp -o GappyPairC.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c KernelUtils.cpp -o KernelUtils.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MismatchC.cpp -o MismatchC.o MismatchC.cpp: In function 'SEXPREC* getMismatchKernelMatrix(Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, bool, bool, int, int, bool, bool, int, alphaInfo*)': MismatchC.cpp:432:41: warning: 'currValSqrt' may be used uninitialized in this function [-Wmaybe-uninitialized] km(i,j) = kernelVal / currValSqrt; ~~~~~~~~~~^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MotifC.cpp -o MotifC.o MotifC.cpp: In function 'void genPredProfileMotif(Rcpp::NumericMatrix, ByteStringVector, Rcpp::IntegerVector, int, ByteStringVector, ByteStringVector, int, bool, int, int, int, int, Rcpp::NumericMatrix, int, ByteStringVector, Rcpp::IntegerVector*, int, int, ByteStringVector, Rcpp::IntegerVector*, int, int, int, bool, bool, bool)': MotifC.cpp:3677:18: warning: 'keyPool' may be used uninitialized in this function [-Wmaybe-uninitialized] pKeypool = keyPool; ~~~~~~~~~^~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PredictionC.cpp -o PredictionC.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PredictionProfileC.cpp -o PredictionProfileC.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_kebabs.cpp -o R_init_kebabs.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rsvm.c -o Rsvm.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SparseMatrixHash.cpp -o SparseMatrixHash.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SpectrumC.cpp -o SpectrumC.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SymmetricPairC.cpp -o SymmetricPairC.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Utils.cpp -o Utils.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c svm.cpp -o svm.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o kebabs.dll tmp.def Biostrings_stubs.o ByteStringVector.o ExplicitRepC.o FeatureWeightsPosDepC.o GappyPairC.o IRanges_stubs.o KernelUtils.o MismatchC.o MotifC.o PredictionC.o PredictionProfileC.o R_init_kebabs.o Rsvm.o SparseMatrixHash.o SpectrumC.o SymmetricPairC.o Utils.o XVector_stubs.o svm.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/kebabs.buildbin-libdir/00LOCK-kebabs/00new/kebabs/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'kebabs' finding HTML links ... done BioVector-class html finding level-2 HTML links ... done BioVector html ControlInformation-class html CrossValidationResult-class html CrossValidationResultAccessors html ExplicitRepresentation-class html ExplicitRepresentationAccessors html GappyPairKernel-class html KBModel-class html KBModelAccessors html KernelMatrix-class html KernelMatrixAccessors html LinearKernel html MismatchKernel-class html ModelSelectionResult-class html ModelSelectionResultAccessors html MotifKernel-class html PredictionProfile-class html PredictionProfileAccessors html ROCData-class html ROCDataAccessors html SVMAccess html SVMInformation-class html SequenceKernel-class html SpectrumKernel-class html SymmetricPairKernel-class html annotationSpecificKernel html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/kebabs.buildbin-libdir/00LOCK-kebabs/00new/kebabs/help/annotationSpecificKernel.html computeROCandAUC html evaluatePrediction html explicitRepresentation html featureWeights html gappyPairKernel html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/kebabs.buildbin-libdir/00LOCK-kebabs/00new/kebabs/help/gappyPairKernel.html genRandBioSeqs html getPredProfMixture-methods html getPredictionProfile-methods html heatmap-methods html kbsvm-methods html kebabsCollectInfo html kebabsData html kebabsOverview html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/kebabs.buildbin-libdir/00LOCK-kebabs/00new/kebabs/help/KeBABS.html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/kebabs.buildbin-libdir/00LOCK-kebabs/00new/kebabs/help/kebabs.html mismatchKernel html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/kebabs.buildbin-libdir/00LOCK-kebabs/00new/kebabs/help/mismatchKernel.html motifKernel html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/kebabs.buildbin-libdir/00LOCK-kebabs/00new/kebabs/help/motifKernel.html performCrossValidation-methods html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/kebabs.buildbin-libdir/00LOCK-kebabs/00new/kebabs/help/crossValidation.html performGridSearch html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/kebabs.buildbin-libdir/00LOCK-kebabs/00new/kebabs/help/gridSearch.html performModelSelection html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/kebabs.buildbin-libdir/00LOCK-kebabs/00new/kebabs/help/modelSelection.html plot-methods html positionDependentKernel html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/kebabs.buildbin-libdir/00LOCK-kebabs/00new/kebabs/help/distanceWeightedKernel.html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/kebabs.buildbin-libdir/00LOCK-kebabs/00new/kebabs/help/positionDependentKernel.html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/kebabs.buildbin-libdir/00LOCK-kebabs/00new/kebabs/help/positionSpecificKernel.html predict-methods html sequenceKernel html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/kebabs.buildbin-libdir/00LOCK-kebabs/00new/kebabs/help/sequenceKernel.html show-methods html spectrumKernel html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/kebabs.buildbin-libdir/00LOCK-kebabs/00new/kebabs/help/spectrumKernel.html symmetricPairKernel html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/kebabs.buildbin-libdir/00LOCK-kebabs/00new/kebabs/help/symmetricPairKernel.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 'kebabs' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ByteStringVector.c -o ByteStringVector.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ExplicitRepC.cpp -o ExplicitRepC.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GappyPairC.cpp -o GappyPairC.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c KernelUtils.cpp -o KernelUtils.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MismatchC.cpp -o MismatchC.o MismatchC.cpp: In function 'SEXPREC* getMismatchKernelMatrix(Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, bool, bool, int, int, bool, bool, int, alphaInfo*)': MismatchC.cpp:432:41: warning: 'currValSqrt' may be used uninitialized in this function [-Wmaybe-uninitialized] km(i,j) = kernelVal / currValSqrt; ~~~~~~~~~~^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MotifC.cpp -o MotifC.o MotifC.cpp: In function 'void genPredProfileMotif(Rcpp::NumericMatrix, ByteStringVector, Rcpp::IntegerVector, int, ByteStringVector, ByteStringVector, int, bool, int, int, int, int, Rcpp::NumericMatrix, int, ByteStringVector, Rcpp::IntegerVector*, int, int, ByteStringVector, Rcpp::IntegerVector*, int, int, int, bool, bool, bool)': MotifC.cpp:3677:18: warning: 'keyPool' may be used uninitialized in this function [-Wmaybe-uninitialized] pKeypool = keyPool; ~~~~~~~~~^~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PredictionC.cpp -o PredictionC.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PredictionProfileC.cpp -o PredictionProfileC.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_kebabs.cpp -o R_init_kebabs.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rsvm.c -o Rsvm.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SparseMatrixHash.cpp -o SparseMatrixHash.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SpectrumC.cpp -o SpectrumC.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SymmetricPairC.cpp -o SymmetricPairC.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Utils.cpp -o Utils.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c svm.cpp -o svm.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o kebabs.dll tmp.def Biostrings_stubs.o ByteStringVector.o ExplicitRepC.o FeatureWeightsPosDepC.o GappyPairC.o IRanges_stubs.o KernelUtils.o MismatchC.o MotifC.o PredictionC.o PredictionProfileC.o R_init_kebabs.o Rsvm.o SparseMatrixHash.o SpectrumC.o SymmetricPairC.o Utils.o XVector_stubs.o svm.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/kebabs.buildbin-libdir/kebabs/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'kebabs' as kebabs_1.28.1.zip * DONE (kebabs) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'kebabs' successfully unpacked and MD5 sums checked