Build/check report for BioC 3.23 - INSTALL results for kebabs on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4775
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*
INSTALL results for kebabs on nebbiolo1

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: 1.45.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL kebabs
StartedAt: 2025-11-02 15:21:43 -0500 (Sun, 02 Nov 2025)
EndedAt: 2025-11-02 15:23:17 -0500 (Sun, 02 Nov 2025)
EllapsedTime: 94.2 seconds
RetCode: 0
Status: OK
Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL kebabs
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘kebabs’ ...
** this is package ‘kebabs’ version ‘1.45.0’
** 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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ByteStringVector.c -o ByteStringVector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c ExplicitRepC.cpp -o ExplicitRepC.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c KernelUtils.cpp -o KernelUtils.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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-3.23-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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-3.23-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c PredictionC.cpp -o PredictionC.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c PredictionProfileC.cpp -o PredictionProfileC.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-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.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c Rsvm.c -o Rsvm.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c SparseMatrixHash.cpp -o SparseMatrixHash.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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-3.23-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c SymmetricPairC.cpp -o SymmetricPairC.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c Utils.cpp -o Utils.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c svm.cpp -o svm.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-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-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-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)