Movatterモバイル変換

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:kebabs.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings kebabs_1.44.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/kebabs.Rcheck’* using R version 4.5.2 (2025-10-31)* using platform: x86_64-pc-linux-gnu* R was compiled by    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0* running under: Ubuntu 24.04.3 LTS* using session charset: UTF-8* checking for file ‘kebabs/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘kebabs’ version ‘1.44.0’* checking package namespace information ... OK* checking package dependencies ... OK* checking if this is a source package ... OK* checking if there is a namespace ... OK* checking for hidden files and directories ... OK* checking for portable file names ... OK* checking for sufficient/correct file permissions ... OK* checking whether package ‘kebabs’ can be installed ... OK* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’* checking installed package size ... INFO  installed size is 11.5Mb  sub-directories of 1Mb or more:    R      1.5Mb    data   1.2Mb    libs   8.3Mb* checking package directory ... OK* checking ‘build’ directory ... OK* checking DESCRIPTION meta-information ... OK* checking top-level files ... OK* checking for left-over files ... OK* checking index information ... OK* checking package subdirectories ... OK* checking code files for non-ASCII characters ... OK* checking R files for syntax errors ... OK* checking whether the package can be loaded ... OK* checking whether the package can be loaded with stated dependencies ... OK* checking whether the package can be unloaded cleanly ... OK* checking whether the namespace can be loaded with stated dependencies ... OK* checking whether the namespace can be unloaded cleanly ... OK* checking loading without being on the library search path ... OK* checking whether startup messages can be suppressed ... OK* checking dependencies in R code ... OK* checking S3 generic/method consistency ... OK* checking replacement functions ... OK* checking foreign function calls ... OK* checking R code for possible problems ... OK* checking Rd files ... OK* checking Rd metadata ... OK* checking Rd cross-references ... NOTEFound the following Rd file(s) with Rd \link{} targets missing packageanchors:  BioVector-class.Rd: XStringSet-class  BioVector.Rd: XStringSet, metadata, mcols, elementMetadata,    DNAStringSet, RNAStringSet, AAStringSet  ExplicitRepresentation-class.Rd: dgRMatrix-class  LinearKernel.Rd: dgCMatrix-class  annotationSpecificKernel.Rd: DNAStringSet-class, RNAStringSet-class,    AAStringSet-class, mcols, metadata  explicitRepresentation.Rd: DNAStringSet-class, RNAStringSet-class,    AAStringSet-class  gappyPairKernel.Rd: DNAStringSet-class, RNAStringSet-class,    AAStringSet-class  getPredProfMixture-methods.Rd: DNAString-class, RNAString-class,    AAString-class, DNAStringSet-class, RNAStringSet-class,    AAStringSet-class  getPredictionProfile-methods.Rd: DNAString-class, RNAString-class,    AAString-class, DNAStringSet-class, RNAStringSet-class,    AAStringSet-class  kbsvm-methods.Rd: DNAStringSet-class, RNAStringSet-class,    AAStringSet-class, DNAStringSet, RNAStringSet, AAStringSet,    XStringSet-class  mismatchKernel.Rd: DNAStringSet-class, RNAStringSet-class,    AAStringSet-class  motifKernel.Rd: DNAStringSet-class, RNAStringSet-class,    AAStringSet-class  plot-methods.Rd: mcols  positionDependentKernel.Rd: DNAStringSet-class, RNAStringSet-class,    AAStringSet-class, metadata, mcols  predict-methods.Rd: DNAStringSet-class, RNAStringSet-class,    AAStringSet-class  sequenceKernel.Rd: DNAStringSet-class, RNAStringSet-class,    AAStringSet-class  spectrumKernel.Rd: DNAStringSet-class, RNAStringSet-class,    AAStringSet-classPlease provide package anchors for all Rd \link{} targets not in thepackage itself and the base packages.* checking for missing documentation entries ... OK* checking for code/documentation mismatches ... OK* checking Rd \usage sections ... OK* checking Rd contents ... OK* checking for unstated dependencies in examples ... OK* checking contents of ‘data’ directory ... OK* checking data for non-ASCII characters ... OK* checking data for ASCII and uncompressed saves ... OK* checking line endings in C/C++/Fortran sources/headers ... OK* checking line endings in Makefiles ... OK* checking compilation flags in Makevars ... OK* checking for GNU extensions in Makefiles ... OK* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK* checking use of PKG_*FLAGS in Makefiles ... OK* checking compiled code ... NOTENote: information on .o files is not available* checking files in ‘vignettes’ ... OK* checking examples ... OKExamples with CPU (user + system) or elapsed time > 5s                       user system elapsedperformModelSelection 6.665  0.008   6.673LinearKernel          6.399  0.027   6.428* checking for unstated dependencies in vignettes ... OK* checking package vignettes ... OK* checking re-building of vignette outputs ... OK* checking PDF version of manual ... OK* DONEStatus: 2 NOTEsSee  ‘/home/biocbuild/bbs-3.22-bioc/meat/kebabs.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL kebabs###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘kebabs’ ...** this is package ‘kebabs’ version ‘1.44.0’** using staged installation** libsusing C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c Biostrings_stubs.c -o Biostrings_stubs.ogcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ByteStringVector.c -o ByteStringVector.og++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c ExplicitRepC.cpp -o ExplicitRepC.og++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.og++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c GappyPairC.cpp -o GappyPairC.oIn function ‘void getKMStdAnnGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, int, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = unsigned char]’,    inlined from ‘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)’ at GappyPairC.cpp:3480:33:GappyPairC.cpp:1157:38: warning: ‘y.ByteStringVector::nchar’ may be used uninitialized [-Wmaybe-uninitialized] 1157 |                 seqnchar = y.nchar[iY];      |                            ~~~~~~~~~~^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:3409:25: note: ‘y.ByteStringVector::nchar’ was declared here 3409 |     ByteStringVector x, y, annX, annY, annCharset;      |                         ^In function ‘void getKMStdAnnGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, int, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = unsigned char]’,    inlined from ‘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)’ at GappyPairC.cpp:3480:33:GappyPairC.cpp:1156:34: warning: ‘y.ByteStringVector::ptr’ may be used uninitialized [-Wmaybe-uninitialized] 1156 |                 seqptr = y.ptr[iY];      |                          ~~~~~~~~^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:3409:25: note: ‘y.ByteStringVector::ptr’ was declared here 3409 |     ByteStringVector x, y, annX, annY, annCharset;      |                         ^GappyPairC.cpp:3535:33: warning: ‘annY.ByteStringVector::ptr’ may be used uninitialized [-Wmaybe-uninitialized] 3535 |                 getKMStdAnnGappy(maxUIndex64, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,      |                 ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3536 |                                  k, m, normalized, symmetric, presence, reverseComplement,      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3537 |                                  maxSeqLength, dimFeatureSpace, &alphaInf);      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GappyPairC.cpp:3409:34: note: ‘annY.ByteStringVector::ptr’ was declared here 3409 |     ByteStringVector x, y, annX, annY, annCharset;      |                                  ^~~~GappyPairC.cpp:3535:33: warning: ‘annX.ByteStringVector::ptr’ may be used uninitialized [-Wmaybe-uninitialized] 3535 |                 getKMStdAnnGappy(maxUIndex64, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,      |                 ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3536 |                                  k, m, normalized, symmetric, presence, reverseComplement,      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3537 |                                  maxSeqLength, dimFeatureSpace, &alphaInf);      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GappyPairC.cpp:3409:28: note: ‘annX.ByteStringVector::ptr’ was declared here 3409 |     ByteStringVector x, y, annX, annY, annCharset;      |                            ^~~~gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.og++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c KernelUtils.cpp -o KernelUtils.og++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c MismatchC.cpp -o MismatchC.oMismatchC.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 [-Wmaybe-uninitialized]  432 |                     km(i,j) = kernelVal / currValSqrt;      |                               ~~~~~~~~~~^~~~~~~~~~~~~MismatchC.cpp:368:32: note: ‘currValSqrt’ was declared here  368 |     double kernelVal, currVal, currValSqrt;      |                                ^~~~~~~~~~~g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c MotifC.cpp -o MotifC.oMotifC.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 [-Wmaybe-uninitialized] 3677 |         pKeypool = keyPool;      |         ~~~~~~~~~^~~~~~~~~MotifC.cpp:3514:11: note: ‘keyPool’ was declared here 3514 |     char *keyPool;      |           ^~~~~~~g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c PredictionC.cpp -o PredictionC.og++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c PredictionProfileC.cpp -o PredictionProfileC.og++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c R_init_kebabs.cpp -o R_init_kebabs.ogcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c Rsvm.c -o Rsvm.og++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c SparseMatrixHash.cpp -o SparseMatrixHash.og++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c SpectrumC.cpp -o SpectrumC.oIn function ‘void getKMStdAnnSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = unsigned char]’,    inlined from ‘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)’ at SpectrumC.cpp:3228:32:SpectrumC.cpp:832:38: warning: ‘y.ByteStringVector::nchar’ may be used uninitialized [-Wmaybe-uninitialized]  832 |                 seqnchar = y.nchar[iY];      |                            ~~~~~~~~~~^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:3158:25: note: ‘y.ByteStringVector::nchar’ was declared here 3158 |     ByteStringVector x, y, annX, annY, annCharset;      |                         ^In function ‘void getKMStdAnnSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = unsigned char]’,    inlined from ‘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)’ at SpectrumC.cpp:3228:32:SpectrumC.cpp:831:34: warning: ‘y.ByteStringVector::ptr’ may be used uninitialized [-Wmaybe-uninitialized]  831 |                 seqptr = y.ptr[iY];      |                          ~~~~~~~~^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:3158:25: note: ‘y.ByteStringVector::ptr’ was declared here 3158 |     ByteStringVector x, y, annX, annY, annCharset;      |                         ^SpectrumC.cpp:3283:32: warning: ‘annY.ByteStringVector::ptr’ may be used uninitialized [-Wmaybe-uninitialized] 3283 |                 getKMStdAnnSpec(maxUIndex64, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,      |                 ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3284 |                                 k, normalized, symmetric, presence, reverseComplement, maxSeqLength,      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3285 |                                 dimFeatureSpace, &alphaInf);      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~SpectrumC.cpp:3158:34: note: ‘annY.ByteStringVector::ptr’ was declared here 3158 |     ByteStringVector x, y, annX, annY, annCharset;      |                                  ^~~~SpectrumC.cpp:3283:32: warning: ‘annX.ByteStringVector::ptr’ may be used uninitialized [-Wmaybe-uninitialized] 3283 |                 getKMStdAnnSpec(maxUIndex64, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,      |                 ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3284 |                                 k, normalized, symmetric, presence, reverseComplement, maxSeqLength,      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3285 |                                 dimFeatureSpace, &alphaInf);      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~SpectrumC.cpp:3158:28: note: ‘annX.ByteStringVector::ptr’ was declared here 3158 |     ByteStringVector x, y, annX, annY, annCharset;      |                            ^~~~g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c SymmetricPairC.cpp -o SymmetricPairC.og++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c Utils.cpp -o Utils.ogcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.og++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c svm.cpp -o svm.og++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-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-3.22-bioc/R/lib -lRinstalling to /home/biocbuild/bbs-3.22-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)