##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:kebabs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings kebabs_1.45.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/kebabs.Rcheck’
* using R Under development (unstable) (2026-03-20 r89666)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-03-21 03:34:43 UTC
* using option ‘--no-vignettes’
* checking for file ‘kebabs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘kebabs’ version ‘1.45.0’
* 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: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.sdk’
* checking installed package size ... OK
* 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  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-class
Please provide package anchors for all Rd \link{} targets not in the
package 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 ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/kebabs.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL kebabs
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘kebabs’ ...
** this is package ‘kebabs’ version ‘1.45.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ByteStringVector.c -o ByteStringVector.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c ExplicitRepC.cpp -o ExplicitRepC.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c GappyPairC.cpp -o GappyPairC.o
GappyPairC.cpp:909:50: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  909 |     int maxNoOfNodes, seqnchar, currStack, stack[8*k];
      |                                                  ^~~
GappyPairC.cpp:909:52: note: function parameter 'k' with unknown value cannot be used in a constant expression
  909 |     int maxNoOfNodes, seqnchar, currStack, stack[8*k];
      |                                                    ^
GappyPairC.cpp:902:27: note: declared here
  902 |                       int k, int m, bool normalized, bool symmetric, bool presence,
      |                           ^
GappyPairC.cpp:2677:36: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 2677 |     int i, j, iX, currStack, stack[8*k];
      |                                    ^~~
GappyPairC.cpp:2677:38: note: function parameter 'k' with unknown value cannot be used in a constant expression
 2677 |     int i, j, iX, currStack, stack[8*k];
      |                                      ^
GappyPairC.cpp:2669:63: note: declared here
 2669 |                  ByteStringVector annX, int maxSeqLength, int k, int m, bool normalized,
      |                                                               ^
GappyPairC.cpp:2959:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 2959 |     char kmer[2 * k + m + 1 + kmerOffset]; // add char for \0
      |               ^~~~~~~~~~~~~~~~~~~~~~~~~~
GappyPairC.cpp:2959:19: note: function parameter 'k' with unknown value cannot be used in a constant expression
 2959 |     char kmer[2 * k + m + 1 + kmerOffset]; // add char for \0
      |                   ^
GappyPairC.cpp:2930:67: note: declared here
 2930 | static void assignFeatureNames(SEXP colnames, void *indexMap, int k, int m, struct alphaInfo *alphaInf,
      |                                                                   ^
GappyPairC.cpp:4297:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 4297 |     char kmer[k + 1], position[12];
      |               ^~~~~
GappyPairC.cpp:4297:15: note: function parameter 'k' with unknown value cannot be used in a constant expression
GappyPairC.cpp:4292:109: note: declared here
 4292 |                                   NumericVector distWeight, bool reverseComplement, double weightLimit, int k,
      |                                                                                                             ^
GappyPairC.cpp:909:50: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  909 |     int maxNoOfNodes, seqnchar, currStack, stack[8*k];
      |                                                  ^~~
GappyPairC.cpp:3480:17: note: in instantiation of function template specialization 'getKMStdAnnGappy<unsigned char>' requested here
 3480 |                 getKMStdAnnGappy(maxUIndex8, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
      |                 ^
GappyPairC.cpp:909:52: note: function parameter 'k' with unknown value cannot be used in a constant expression
  909 |     int maxNoOfNodes, seqnchar, currStack, stack[8*k];
      |                                                    ^
GappyPairC.cpp:902:27: note: declared here
  902 |                       int k, int m, bool normalized, bool symmetric, bool presence,
      |                           ^
GappyPairC.cpp:909:50: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  909 |     int maxNoOfNodes, seqnchar, currStack, stack[8*k];
      |                                                  ^~~
GappyPairC.cpp:3498:17: note: in instantiation of function template specialization 'getKMStdAnnGappy<unsigned short>' requested here
 3498 |                 getKMStdAnnGappy(maxUIndex16, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
      |                 ^
GappyPairC.cpp:909:52: note: function parameter 'k' with unknown value cannot be used in a constant expression
  909 |     int maxNoOfNodes, seqnchar, currStack, stack[8*k];
      |                                                    ^
GappyPairC.cpp:902:27: note: declared here
  902 |                       int k, int m, bool normalized, bool symmetric, bool presence,
      |                           ^
GappyPairC.cpp:909:50: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  909 |     int maxNoOfNodes, seqnchar, currStack, stack[8*k];
      |                                                  ^~~
GappyPairC.cpp:3517:17: note: in instantiation of function template specialization 'getKMStdAnnGappy<unsigned int>' requested here
 3517 |                 getKMStdAnnGappy(maxUIndex32, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
      |                 ^
GappyPairC.cpp:909:52: note: function parameter 'k' with unknown value cannot be used in a constant expression
  909 |     int maxNoOfNodes, seqnchar, currStack, stack[8*k];
      |                                                    ^
GappyPairC.cpp:902:27: note: declared here
  902 |                       int k, int m, bool normalized, bool symmetric, bool presence,
      |                           ^
GappyPairC.cpp:909:50: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  909 |     int maxNoOfNodes, seqnchar, currStack, stack[8*k];
      |                                                  ^~~
GappyPairC.cpp:3535:17: note: in instantiation of function template specialization 'getKMStdAnnGappy<unsigned long long>' requested here
 3535 |                 getKMStdAnnGappy(maxUIndex64, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
      |                 ^
GappyPairC.cpp:909:52: note: function parameter 'k' with unknown value cannot be used in a constant expression
  909 |     int maxNoOfNodes, seqnchar, currStack, stack[8*k];
      |                                                    ^
GappyPairC.cpp:902:27: note: declared here
  902 |                       int k, int m, bool normalized, bool symmetric, bool presence,
      |                           ^
GappyPairC.cpp:4297:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 4297 |     char kmer[k + 1], position[12];
      |               ^~~~~
GappyPairC.cpp:4398:13: note: in instantiation of function template specialization 'getWeightedFeatOfSVGappyPair<unsigned char>' requested here
 4398 |             getWeightedFeatOfSVGappyPair(maxUIndex8, pdFeatWeights, pdfwmap, pdfimap, x, sizeX, selX, offsetX, maxSeqLength,
      |             ^
GappyPairC.cpp:4297:15: note: function parameter 'k' with unknown value cannot be used in a constant expression
 4297 |     char kmer[k + 1], position[12];
      |               ^
GappyPairC.cpp:4292:109: note: declared here
 4292 |                                   NumericVector distWeight, bool reverseComplement, double weightLimit, int k,
      |                                                                                                             ^
GappyPairC.cpp:4297:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 4297 |     char kmer[k + 1], position[12];
      |               ^~~~~
GappyPairC.cpp:4406:13: note: in instantiation of function template specialization 'getWeightedFeatOfSVGappyPair<unsigned short>' requested here
 4406 |             getWeightedFeatOfSVGappyPair(maxUIndex16, pdFeatWeights, pdfwmap, pdfimap, x, sizeX, selX, offsetX, maxSeqLength,
      |             ^
GappyPairC.cpp:4297:15: note: function parameter 'k' with unknown value cannot be used in a constant expression
 4297 |     char kmer[k + 1], position[12];
      |               ^
GappyPairC.cpp:4292:109: note: declared here
 4292 |                                   NumericVector distWeight, bool reverseComplement, double weightLimit, int k,
      |                                                                                                             ^
GappyPairC.cpp:4297:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 4297 |     char kmer[k + 1], position[12];
      |               ^~~~~
GappyPairC.cpp:4415:13: note: in instantiation of function template specialization 'getWeightedFeatOfSVGappyPair<unsigned int>' requested here
 4415 |             getWeightedFeatOfSVGappyPair(maxUIndex32, pdFeatWeights, pdfwmap, pdfimap, x, sizeX, selX, offsetX, maxSeqLength,
      |             ^
GappyPairC.cpp:4297:15: note: function parameter 'k' with unknown value cannot be used in a constant expression
 4297 |     char kmer[k + 1], position[12];
      |               ^
GappyPairC.cpp:4292:109: note: declared here
 4292 |                                   NumericVector distWeight, bool reverseComplement, double weightLimit, int k,
      |                                                                                                             ^
GappyPairC.cpp:4297:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 4297 |     char kmer[k + 1], position[12];
      |               ^~~~~
GappyPairC.cpp:4423:13: note: in instantiation of function template specialization 'getWeightedFeatOfSVGappyPair<unsigned long long>' requested here
 4423 |             getWeightedFeatOfSVGappyPair(maxUIndex64, pdFeatWeights, pdfwmap, pdfimap, x, sizeX, selX, offsetX, maxSeqLength,
      |             ^
GappyPairC.cpp:4297:15: note: function parameter 'k' with unknown value cannot be used in a constant expression
 4297 |     char kmer[k + 1], position[12];
      |               ^
GappyPairC.cpp:4292:109: note: declared here
 4292 |                                   NumericVector distWeight, bool reverseComplement, double weightLimit, int k,
      |                                                                                                             ^
12 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c KernelUtils.cpp -o KernelUtils.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MismatchC.cpp -o MismatchC.o
MismatchC.cpp:565:40: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  565 |     uint32_t low, featureStored, stack[6*intf->k], currCount;
      |                                        ^~~~~~~~~
MismatchC.cpp:565:42: note: function parameter 'intf' with unknown value cannot be used in a constant expression
  565 |     uint32_t low, featureStored, stack[6*intf->k], currCount;
      |                                          ^
MismatchC.cpp:562:80: note: declared here
  562 | void mutateFeatureIndexViaArray(uint64_t featureIndex, struct ifMutateFeature *intf)
      |                                                                                ^
MismatchC.cpp:735:23: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  735 |     uint32_t i, stack[6*intf->k], low, featureStored, colIndex, currCount;
      |                       ^~~~~~~~~
MismatchC.cpp:735:25: note: function parameter 'intf' with unknown value cannot be used in a constant expression
  735 |     uint32_t i, stack[6*intf->k], low, featureStored, colIndex, currCount;
      |                         ^
MismatchC.cpp:732:72: note: declared here
  732 | void mutateFeatureIndex(uint64_t featureIndex, struct ifMutateFeature *intf)
      |                                                                        ^
MismatchC.cpp:1534:73: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 1534 |     int currBlock, currIndex, newBlock, maxBlockIndex, currStack, stack[2*k];
      |                                                                         ^~~
MismatchC.cpp:1534:75: note: function parameter 'k' with unknown value cannot be used in a constant expression
 1534 |     int currBlock, currIndex, newBlock, maxBlockIndex, currStack, stack[2*k];
      |                                                                           ^
MismatchC.cpp:1530:100: note: declared here
 1530 | void storeFeatures(struct prefTree *pTree, SEXP slot_p, SEXP slot_j, SEXP slot_x, int *jIndex, int k,
      |                                                                                                    ^
MismatchC.cpp:1734:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 1734 |     char kmer[k + 1]; // add char for \0
      |               ^~~~~
MismatchC.cpp:1734:15: note: function parameter 'k' with unknown value cannot be used in a constant expression
MismatchC.cpp:1727:60: note: declared here
 1727 | void assignFeatureNames(SEXP colnames, void *indexMap, int k, struct alphaInfo *alphaInf, uint64_t dimFeatureSpace,
      |                                                            ^
MismatchC.cpp:2144:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 2144 |     uint32_t stack[6*k], low, currCount;
      |                    ^~~
MismatchC.cpp:2144:22: note: function parameter 'k' with unknown value cannot be used in a constant expression
 2144 |     uint32_t stack[6*k], low, currCount;
      |                      ^
MismatchC.cpp:2139:104: note: declared here
 2139 | void mutateFeatureIndexPredProf(uint64_t featureIndex, int svmIndex, int sampleIndex, int currPos, int k, int m,
      |                                                                                                        ^
MismatchC.cpp:2146:38: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 2146 |     bool finished, mismatchPositions[k];
      |                                      ^
MismatchC.cpp:2146:38: note: function parameter 'k' with unknown value cannot be used in a constant expression
MismatchC.cpp:2139:104: note: declared here
 2139 | void mutateFeatureIndexPredProf(uint64_t featureIndex, int svmIndex, int sampleIndex, int currPos, int k, int m,
      |                                                                                                        ^
6 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MotifC.cpp -o MotifC.o
MotifC.cpp:241:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  241 |     char kmer[k];
      |               ^
MotifC.cpp:241:15: note: function parameter 'k' with unknown value cannot be used in a constant expression
MotifC.cpp:239:53: note: declared here
  239 | void listTreeMotif(struct prefTreeMotif *pTree, int k, struct alphaInfo *alphaInf)
      |                                                     ^
MotifC.cpp:704:50: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  704 |     char *pKey, localKey[1024], digit, currMotif[2 * maxPatternLength + 1]; // including annotation chars
      |                                                  ^~~~~~~~~~~~~~~~~~~~~~~~
MotifC.cpp:704:54: note: function parameter 'maxPatternLength' with unknown value cannot be used in a constant expression
  704 |     char *pKey, localKey[1024], digit, currMotif[2 * maxPatternLength + 1]; // including annotation chars
      |                                                      ^
MotifC.cpp:697:75: note: declared here
  697 | void setFeatureIndex(struct prefTreeMotif *pTree, int maxMotifLength, int maxPatternLength, struct alphaInfo *alphaInf,
      |                                                                           ^
MotifC.cpp:866:36: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  866 |     uint32_t currBlock, blockStack[4 * (maxMotifLength + 1)];
      |                                    ^~~~~~~~~~~~~~~~~~~~~~~~
MotifC.cpp:866:41: note: function parameter 'maxMotifLength' with unknown value cannot be used in a constant expression
  866 |     uint32_t currBlock, blockStack[4 * (maxMotifLength + 1)];
      |                                         ^
MotifC.cpp:864:26: note: declared here
  864 |                      int maxMotifLength, struct alphaInfo *alphaInf, bool zeroFeatures)
      |                          ^
MotifC.cpp:1734:25: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 1734 |     uint32_t blockStack[4 * (2 * maxMotifLength + 1)];
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
MotifC.cpp:1734:34: note: function parameter 'maxMotifLength' with unknown value cannot be used in a constant expression
 1734 |     uint32_t blockStack[4 * (2 * maxMotifLength + 1)];
      |                                  ^
MotifC.cpp:1731:77: note: declared here
 1731 |                       uint32_t sampleIndex, struct alphaInfo *alphaInf, int maxMotifLength)
      |                                                                             ^
MotifC.cpp:1860:36: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 1860 |     uint32_t currBlock, blockStack[4 * (maxMotifLength + 1)];
      |                                    ^~~~~~~~~~~~~~~~~~~~~~~~
MotifC.cpp:1860:41: note: function parameter 'maxMotifLength' with unknown value cannot be used in a constant expression
 1860 |     uint32_t currBlock, blockStack[4 * (maxMotifLength + 1)];
      |                                         ^
MotifC.cpp:1857:30: note: declared here
 1857 |                          int maxMotifLength, uint32_t sampleIndex, int numUsedFeatures, SEXP slot_j, SEXP slot_x, int *jIdx,
      |                              ^
MotifC.cpp:2927:14: warning: variable 'dimFeatureSpace' set but not used [-Wunused-but-set-variable]
 2927 |     uint64_t dimFeatureSpace;
      |              ^
MotifC.cpp:3351:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 3351 |     char kmer[maxPatternLength + 1], position[12];
      |               ^~~~~~~~~~~~~~~~~~~~
MotifC.cpp:3351:15: note: function parameter 'maxPatternLength' with unknown value cannot be used in a constant expression
MotifC.cpp:3346:83: note: declared here
 3346 |                               IntegerVector motifLengths, int maxMotifLength, int maxPatternLength,
      |                                                                                   ^
MotifC.cpp:3511:41: warning: variable 'dimFeatureSpace' set but not used [-Wunused-but-set-variable]
 3511 |     uint64_t keyPoolSize, poolNextFree, dimFeatureSpace;
      |                                         ^
MotifC.cpp:3351:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 3351 |     char kmer[maxPatternLength + 1], position[12];
      |               ^~~~~~~~~~~~~~~~~~~~
MotifC.cpp:3433:13: note: in instantiation of function template specialization 'getWeightedFeatOfSVMotif<unsigned char>' requested here
 3433 |             getWeightedFeatOfSVMotif(maxUIndex8, pdFeatWeights, pdfwmap, pdfimap, x, sizeX, selX, offsetX, maxSeqLength,
      |             ^
MotifC.cpp:3351:15: note: function parameter 'maxPatternLength' with unknown value cannot be used in a constant expression
 3351 |     char kmer[maxPatternLength + 1], position[12];
      |               ^
MotifC.cpp:3346:83: note: declared here
 3346 |                               IntegerVector motifLengths, int maxMotifLength, int maxPatternLength,
      |                                                                                   ^
MotifC.cpp:3351:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 3351 |     char kmer[maxPatternLength + 1], position[12];
      |               ^~~~~~~~~~~~~~~~~~~~
MotifC.cpp:3442:13: note: in instantiation of function template specialization 'getWeightedFeatOfSVMotif<unsigned short>' requested here
 3442 |             getWeightedFeatOfSVMotif(maxUIndex16, pdFeatWeights, pdfwmap, pdfimap, x, sizeX, selX, offsetX, maxSeqLength,
      |             ^
MotifC.cpp:3351:15: note: function parameter 'maxPatternLength' with unknown value cannot be used in a constant expression
 3351 |     char kmer[maxPatternLength + 1], position[12];
      |               ^
MotifC.cpp:3346:83: note: declared here
 3346 |                               IntegerVector motifLengths, int maxMotifLength, int maxPatternLength,
      |                                                                                   ^
MotifC.cpp:3351:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 3351 |     char kmer[maxPatternLength + 1], position[12];
      |               ^~~~~~~~~~~~~~~~~~~~
MotifC.cpp:3452:13: note: in instantiation of function template specialization 'getWeightedFeatOfSVMotif<unsigned int>' requested here
 3452 |             getWeightedFeatOfSVMotif(maxUIndex32, pdFeatWeights, pdfwmap, pdfimap, x, sizeX, selX, offsetX, maxSeqLength,
      |             ^
MotifC.cpp:3351:15: note: function parameter 'maxPatternLength' with unknown value cannot be used in a constant expression
 3351 |     char kmer[maxPatternLength + 1], position[12];
      |               ^
MotifC.cpp:3346:83: note: declared here
 3346 |                               IntegerVector motifLengths, int maxMotifLength, int maxPatternLength,
      |                                                                                   ^
MotifC.cpp:3351:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 3351 |     char kmer[maxPatternLength + 1], position[12];
      |               ^~~~~~~~~~~~~~~~~~~~
MotifC.cpp:3461:13: note: in instantiation of function template specialization 'getWeightedFeatOfSVMotif<unsigned long long>' requested here
 3461 |             getWeightedFeatOfSVMotif(maxUIndex64, pdFeatWeights, pdfwmap, pdfimap, x, sizeX, selX, offsetX, maxSeqLength,
      |             ^
MotifC.cpp:3351:15: note: function parameter 'maxPatternLength' with unknown value cannot be used in a constant expression
 3351 |     char kmer[maxPatternLength + 1], position[12];
      |               ^
MotifC.cpp:3346:83: note: declared here
 3346 |                               IntegerVector motifLengths, int maxMotifLength, int maxPatternLength,
      |                                                                                   ^
12 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c PredictionC.cpp -o PredictionC.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c PredictionProfileC.cpp -o PredictionProfileC.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c R_init_kebabs.cpp -o R_init_kebabs.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Rsvm.c -o Rsvm.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c SparseMatrixHash.cpp -o SparseMatrixHash.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c SpectrumC.cpp -o SpectrumC.o
SpectrumC.cpp:588:35: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  588 |     int i, j, l, currStack, stack[4*k], iX, iY, twoK, elemIndex, maxNoOfNodes, noSamples = sizeX;
      |                                   ^~~
SpectrumC.cpp:588:37: note: function parameter 'k' with unknown value cannot be used in a constant expression
  588 |     int i, j, l, currStack, stack[4*k], iX, iY, twoK, elemIndex, maxNoOfNodes, noSamples = sizeX;
      |                                     ^
SpectrumC.cpp:583:26: note: declared here
  583 |                      int k, bool normalized,  bool symmetric, bool presence,
      |                          ^
SpectrumC.cpp:2418:70: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 2418 |     int lastBlockSize, maxBlockIndex, maxNoOfNodes, currStack, stack[4*k];
      |                                                                      ^~~
SpectrumC.cpp:2418:72: note: function parameter 'k' with unknown value cannot be used in a constant expression
 2418 |     int lastBlockSize, maxBlockIndex, maxNoOfNodes, currStack, stack[4*k];
      |                                                                        ^
SpectrumC.cpp:2409:66: note: declared here
 2409 |                     ByteStringVector annX, int maxSeqLength, int k, bool normalized,
      |                                                                  ^
SpectrumC.cpp:2780:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 2780 |     char kmer[k + 1 + kmerOffset]; // additional chars: annotation and \0
      |               ^~~~~~~~~~~~~~~~~~
SpectrumC.cpp:2780:15: note: function parameter 'k' with unknown value cannot be used in a constant expression
SpectrumC.cpp:2751:67: note: declared here
 2751 | static void assignFeatureNames(SEXP colnames, void *indexMap, int k, struct alphaInfo *alphaInf, uint64_t dimFeatureSpace,
      |                                                                   ^
SpectrumC.cpp:3860:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 3860 |     char kmer[k + 1], position[12];
      |               ^~~~~
SpectrumC.cpp:3860:15: note: function parameter 'k' with unknown value cannot be used in a constant expression
SpectrumC.cpp:3856:38: note: declared here
 3856 |                                  int k, int minPos, int maxPos, struct alphaInfo *alphaInf, bool normalized,
      |                                      ^
SpectrumC.cpp:588:35: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  588 |     int i, j, l, currStack, stack[4*k], iX, iY, twoK, elemIndex, maxNoOfNodes, noSamples = sizeX;
      |                                   ^~~
SpectrumC.cpp:3228:17: note: in instantiation of function template specialization 'getKMStdAnnSpec<unsigned char>' requested here
 3228 |                 getKMStdAnnSpec(maxUIndex8, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
      |                 ^
SpectrumC.cpp:588:37: note: function parameter 'k' with unknown value cannot be used in a constant expression
  588 |     int i, j, l, currStack, stack[4*k], iX, iY, twoK, elemIndex, maxNoOfNodes, noSamples = sizeX;
      |                                     ^
SpectrumC.cpp:583:26: note: declared here
  583 |                      int k, bool normalized,  bool symmetric, bool presence,
      |                          ^
SpectrumC.cpp:588:35: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  588 |     int i, j, l, currStack, stack[4*k], iX, iY, twoK, elemIndex, maxNoOfNodes, noSamples = sizeX;
      |                                   ^~~
SpectrumC.cpp:3246:17: note: in instantiation of function template specialization 'getKMStdAnnSpec<unsigned short>' requested here
 3246 |                 getKMStdAnnSpec(maxUIndex16, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
      |                 ^
SpectrumC.cpp:588:37: note: function parameter 'k' with unknown value cannot be used in a constant expression
  588 |     int i, j, l, currStack, stack[4*k], iX, iY, twoK, elemIndex, maxNoOfNodes, noSamples = sizeX;
      |                                     ^
SpectrumC.cpp:583:26: note: declared here
  583 |                      int k, bool normalized,  bool symmetric, bool presence,
      |                          ^
SpectrumC.cpp:588:35: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  588 |     int i, j, l, currStack, stack[4*k], iX, iY, twoK, elemIndex, maxNoOfNodes, noSamples = sizeX;
      |                                   ^~~
SpectrumC.cpp:3265:17: note: in instantiation of function template specialization 'getKMStdAnnSpec<unsigned int>' requested here
 3265 |                 getKMStdAnnSpec(maxUIndex32, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
      |                 ^
SpectrumC.cpp:588:37: note: function parameter 'k' with unknown value cannot be used in a constant expression
  588 |     int i, j, l, currStack, stack[4*k], iX, iY, twoK, elemIndex, maxNoOfNodes, noSamples = sizeX;
      |                                     ^
SpectrumC.cpp:583:26: note: declared here
  583 |                      int k, bool normalized,  bool symmetric, bool presence,
      |                          ^
SpectrumC.cpp:588:35: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  588 |     int i, j, l, currStack, stack[4*k], iX, iY, twoK, elemIndex, maxNoOfNodes, noSamples = sizeX;
      |                                   ^~~
SpectrumC.cpp:3283:17: note: in instantiation of function template specialization 'getKMStdAnnSpec<unsigned long long>' requested here
 3283 |                 getKMStdAnnSpec(maxUIndex64, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
      |                 ^
SpectrumC.cpp:588:37: note: function parameter 'k' with unknown value cannot be used in a constant expression
  588 |     int i, j, l, currStack, stack[4*k], iX, iY, twoK, elemIndex, maxNoOfNodes, noSamples = sizeX;
      |                                     ^
SpectrumC.cpp:583:26: note: declared here
  583 |                      int k, bool normalized,  bool symmetric, bool presence,
      |                          ^
SpectrumC.cpp:3860:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 3860 |     char kmer[k + 1], position[12];
      |               ^~~~~
SpectrumC.cpp:3951:13: note: in instantiation of function template specialization 'getWeightedFeatOfSVSpectrum<unsigned char>' requested here
 3951 |             getWeightedFeatOfSVSpectrum(maxUIndex8, pdFeatWeights, pdfwmap, pdfimap, x, sizeX, selX, offsetX, maxSeqLength,
      |             ^
SpectrumC.cpp:3860:15: note: function parameter 'k' with unknown value cannot be used in a constant expression
 3860 |     char kmer[k + 1], position[12];
      |               ^
SpectrumC.cpp:3856:38: note: declared here
 3856 |                                  int k, int minPos, int maxPos, struct alphaInfo *alphaInf, bool normalized,
      |                                      ^
SpectrumC.cpp:3860:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 3860 |     char kmer[k + 1], position[12];
      |               ^~~~~
SpectrumC.cpp:3959:13: note: in instantiation of function template specialization 'getWeightedFeatOfSVSpectrum<unsigned short>' requested here
 3959 |             getWeightedFeatOfSVSpectrum(maxUIndex16, pdFeatWeights, pdfwmap, pdfimap, x, sizeX, selX, offsetX, maxSeqLength,
      |             ^
SpectrumC.cpp:3860:15: note: function parameter 'k' with unknown value cannot be used in a constant expression
 3860 |     char kmer[k + 1], position[12];
      |               ^
SpectrumC.cpp:3856:38: note: declared here
 3856 |                                  int k, int minPos, int maxPos, struct alphaInfo *alphaInf, bool normalized,
      |                                      ^
SpectrumC.cpp:3860:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 3860 |     char kmer[k + 1], position[12];
      |               ^~~~~
SpectrumC.cpp:3968:13: note: in instantiation of function template specialization 'getWeightedFeatOfSVSpectrum<unsigned int>' requested here
 3968 |             getWeightedFeatOfSVSpectrum(maxUIndex32, pdFeatWeights, pdfwmap, pdfimap, x, sizeX, selX, offsetX, maxSeqLength,
      |             ^
SpectrumC.cpp:3860:15: note: function parameter 'k' with unknown value cannot be used in a constant expression
 3860 |     char kmer[k + 1], position[12];
      |               ^
SpectrumC.cpp:3856:38: note: declared here
 3856 |                                  int k, int minPos, int maxPos, struct alphaInfo *alphaInf, bool normalized,
      |                                      ^
SpectrumC.cpp:3860:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
 3860 |     char kmer[k + 1], position[12];
      |               ^~~~~
SpectrumC.cpp:3976:13: note: in instantiation of function template specialization 'getWeightedFeatOfSVSpectrum<unsigned long long>' requested here
 3976 |             getWeightedFeatOfSVSpectrum(maxUIndex64, pdFeatWeights, pdfwmap, pdfimap, x, sizeX, selX, offsetX, maxSeqLength,
      |             ^
SpectrumC.cpp:3860:15: note: function parameter 'k' with unknown value cannot be used in a constant expression
 3860 |     char kmer[k + 1], position[12];
      |               ^
SpectrumC.cpp:3856:38: note: declared here
 3856 |                                  int k, int minPos, int maxPos, struct alphaInfo *alphaInf, bool normalized,
      |                                      ^
12 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c SymmetricPairC.cpp -o SymmetricPairC.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Utils.cpp -o Utils.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c svm.cpp -o svm.o
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/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)