############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL kebabs ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘kebabs’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c ByteStringVector.c -o ByteStringVector.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c ExplicitRepC.cpp -o ExplicitRepC.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -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:994:37: warning: ‘annX.ByteStringVector::ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 994 | annptr = annX.ptr[iX]; | ~~~~~~~~~~~^ GappyPairC.cpp:3409:28: note: ‘annX.ByteStringVector::ptr’ was declared here 3409 | ByteStringVector x, y, annX, annY, annCharset; | ^~~~ GappyPairC.cpp:1160:41: warning: ‘annY.ByteStringVector::ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1160 | annptr = annY.ptr[iY]; | ~~~~~~~~~~~^ GappyPairC.cpp:3409:34: note: ‘annY.ByteStringVector::ptr’ was declared here 3409 | ByteStringVector x, y, annX, annY, annCharset; | ^~~~ GappyPairC.cpp:3474:34: warning: ‘y.ByteStringVector::ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 3474 | getKMPosDistGappy(maxUIndex8, km, x, y, sizeX, sizeY, selX, selY, offsetX, offsetY, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3475 | k, m, normalized, symmetric, reverseComplement, posSpec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3476 | distWeight, maxSeqLength, &alphaInf); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GappyPairC.cpp:3474:34: warning: ‘y.ByteStringVector::nchar’ may be used uninitialized in this function [-Wmaybe-uninitialized] gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c KernelUtils.cpp -o KernelUtils.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c MismatchC.cpp -o MismatchC.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -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++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c PredictionC.cpp -o PredictionC.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c PredictionProfileC.cpp -o PredictionProfileC.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_kebabs.cpp -o R_init_kebabs.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c Rsvm.c -o Rsvm.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c SparseMatrixHash.cpp -o SparseMatrixHash.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -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: ‘annX.ByteStringVector::ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 679 | annptr = annX.ptr[iX]; | ~~~~~~~~~~~^ SpectrumC.cpp:3158:28: note: ‘annX.ByteStringVector::ptr’ was declared here 3158 | ByteStringVector x, y, annX, annY, annCharset; | ^~~~ SpectrumC.cpp:835:41: warning: ‘annY.ByteStringVector::ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 835 | annptr = annY.ptr[iY]; | ~~~~~~~~~~~^ SpectrumC.cpp:3158:34: note: ‘annY.ByteStringVector::ptr’ was declared here 3158 | ByteStringVector x, y, annX, annY, annCharset; | ^~~~ SpectrumC.cpp:3222:33: warning: ‘y.ByteStringVector::ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized] 3222 | getKMPosDistSpec(maxUIndex8, km, x, y, sizeX, sizeY, selX, selY, offsetX, offsetY, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3223 | k, normalized, symmetric, reverseComplement, posSpec, distWeight, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3224 | maxSeqLength, &alphaInf); | ~~~~~~~~~~~~~~~~~~~~~~~~ SpectrumC.cpp:3222:33: warning: ‘y.ByteStringVector::nchar’ may be used uninitialized in this function [-Wmaybe-uninitialized] g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c SymmetricPairC.cpp -o SymmetricPairC.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c Utils.cpp -o Utils.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -c svm.cpp -o svm.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o kebabs.so 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 -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-kebabs/00new/kebabs/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (kebabs)