Multiple platform build/check report for BioC 3.20 - CHECK results for kebabs on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for kebabs on nebbiolo2

To the developers/maintainers of the kebabs package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/kebabs.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: kebabs

Version: 1.40.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:kebabs.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings kebabs_1.40.0.tar.gz

StartedAt: 2024-12-20 01:43:22 -0500 (Fri, 20 Dec 2024)

EndedAt: 2024-12-20 01:52:02 -0500 (Fri, 20 Dec 2024)

EllapsedTime: 519.4 seconds

RetCode: 0

Status: OK

CheckDir: kebabs.Rcheck

Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:kebabs.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings kebabs_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/kebabs.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘kebabs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘kebabs’ version ‘1.40.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... NOTE
  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 ... OK
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
LinearKernel          6.337  0.026   6.364
performModelSelection 6.075  0.012   6.088
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/kebabs.Rcheck/00check.log’
for details.

Installation output

kebabs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL kebabs
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘kebabs’ ...
** using staged installation
** libs
using 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 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c GappyPairC.cpp -o GappyPairC.o
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: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 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -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 [-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-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-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 [-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-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c SpectrumC.cpp -o SpectrumC.o
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: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-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-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-3.20-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-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-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)

Tests output

Example timings

kebabs.Rcheck/kebabs-Ex.timings

name	user	system	elapsed
BioVector	0.391	0.000	0.391
CrossValidationResultAccessors	0.001	0.000	0.001
KBModelAccessors	0.000	0.000	0.001
KernelMatrixAccessors	0.001	0.000	0.001
LinearKernel	6.337	0.026	6.364
ModelSelectionResultAccessors	0.000	0.000	0.001
PredictionProfileAccessors	0.001	0.000	0.002
ROCDataAccessors	0.001	0.000	0.000
SVMAccess	0.091	0.002	0.093
annotationSpecificKernel	0.095	0.000	0.095
computeROCandAUC	0.401	0.023	0.424
evaluatePrediction	0.350	0.008	0.359
explicitRepresentation	0.141	0.018	0.159
featureWeights	0.139	0.005	0.144
gappyPairKernel	0.007	0.000	0.006
genRandBioSeqs	0.048	0.001	0.049
getPredProfMixture-methods	2.763	0.204	2.966
getPredictionProfile-methods	0.515	0.067	0.583
heatmap-methods	0.346	0.056	0.402
kbsvm-methods	0.134	0.013	0.148
kebabsCollectInfo	0.013	0.006	0.024
kebabsOverview	0.188	0.007	0.195
mismatchKernel	0.006	0.000	0.006
motifKernel	0.005	0.000	0.006
performCrossValidation-methods	0.141	0.004	0.146
performGridSearch	3.262	0.018	3.281
performModelSelection	6.075	0.012	6.088
plot-methods	0.210	0.006	0.215
positionDependentKernel	0.009	0.000	0.009
predict-methods	0.155	0.004	0.158
sequenceKernel	0.03	0.00	0.03
show-methods	0.020	0.001	0.021
spectrumKernel	0.005	0.000	0.004
symmetricPairKernel	0.104	0.003	0.106