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###
### Running command:
###
### rm -rf kebabs.buildbin-libdir && mkdir kebabs.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh kebabs_1.45.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R kebabs.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=kebabs.buildbin-libdir kebabs_1.45.0.tar.gz'
>>>>>>>
* 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 /Users/biocbuild/bbs-3.23-bioc/meat/kebabs.buildbin-libdir/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)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR kebabs.buildbin-libdir/kebabs/libs/kebabs.so
>>>>>>>
>>>>>>> Paths before fix:
kebabs.buildbin-libdir/kebabs/libs/kebabs.so:
kebabs.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 2000.67.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1356.0.0)
>>>>>>> Fix with install_name_tool:
ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib not found!
