############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL kebabs ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library' * installing *source* package 'kebabs' ... ** using staged installation ** libs gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ByteStringVector.c -o ByteStringVector.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ExplicitRepC.cpp -o ExplicitRepC.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GappyPairC.cpp -o GappyPairC.o GappyPairC.cpp: In function 'SEXPREC* gappyPairKernelMatrixC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': GappyPairC.cpp:3478:33: warning: '*((void*)& annX +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] 3478 | getKMStdAnnGappy(maxUIndex8, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3479 | k, m, normalized, symmetric, presence, reverseComplement, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3480 | maxSeqLength, dimFeatureSpace, &alphaInf); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GappyPairC.cpp:3478:33: warning: '*((void*)& annY +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] GappyPairC.cpp:3472:34: warning: '*((void*)& y +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] 3472 | getKMPosDistGappy(maxUIndex8, km, x, y, sizeX, sizeY, selX, selY, offsetX, offsetY, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3473 | k, m, normalized, symmetric, reverseComplement, posSpec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3474 | distWeight, maxSeqLength, &alphaInf); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GappyPairC.cpp:3472:34: warning: '*((void*)& y +8)' may be used uninitialized in this function [-Wmaybe-uninitialized] gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c KernelUtils.cpp -o KernelUtils.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MismatchC.cpp -o MismatchC.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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] 3677 | pKeypool = keyPool; | ~~~~~~~~~^~~~~~~~~ g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PredictionC.cpp -o PredictionC.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PredictionProfileC.cpp -o PredictionProfileC.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_kebabs.cpp -o R_init_kebabs.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rsvm.c -o Rsvm.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SparseMatrixHash.cpp -o SparseMatrixHash.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SpectrumC.cpp -o SpectrumC.o SpectrumC.cpp: In function 'SEXPREC* spectrumKernelMatrixC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': SpectrumC.cpp:679:37: warning: '*((void*)& annX +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] 679 | annptr = annX.ptr[iX]; | ~~~~~~~~~~~^ SpectrumC.cpp:3156:28: note: '*((void*)& annX +16)' was declared here 3156 | ByteStringVector x, y, annX, annY, annCharset; | ^~~~ SpectrumC.cpp:835:41: warning: '*((void*)& annY +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] 835 | annptr = annY.ptr[iY]; | ~~~~~~~~~~~^ SpectrumC.cpp:3156:34: note: '*((void*)& annY +16)' was declared here 3156 | ByteStringVector x, y, annX, annY, annCharset; | ^~~~ SpectrumC.cpp:3220:33: warning: '*((void*)& y +16)' may be used uninitialized in this function [-Wmaybe-uninitialized] 3220 | getKMPosDistSpec(maxUIndex8, km, x, y, sizeX, sizeY, selX, selY, offsetX, offsetY, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3221 | k, normalized, symmetric, reverseComplement, posSpec, distWeight, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3222 | maxSeqLength, &alphaInf); | ~~~~~~~~~~~~~~~~~~~~~~~~ SpectrumC.cpp:3220:33: warning: '*((void*)& y +8)' may be used uninitialized in this function [-Wmaybe-uninitialized] g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SymmetricPairC.cpp -o SymmetricPairC.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Utils.cpp -o Utils.o gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c svm.cpp -o svm.o g++ -std=gnu++14 -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:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-kebabs/00new/kebabs/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (kebabs)