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###
### Running command:
###
###   rm -rf DNABarcodeCompatibility.buildbin-libdir && mkdir DNABarcodeCompatibility.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DNABarcodeCompatibility_1.27.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R DNABarcodeCompatibility.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DNABarcodeCompatibility.buildbin-libdir DNABarcodeCompatibility_1.27.0.tar.gz'
>>>>>>> 

* installing *source* package ‘DNABarcodeCompatibility’ ...
** this is package ‘DNABarcodeCompatibility’ version ‘1.27.0’
** 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  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c DNABarcodes_init.c -o DNABarcodes_init.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cachedistance.cpp -o cachedistance.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c create_distance_func.cpp -o create_distance_func.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c distance_for_R.cpp -o distance_for_R.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c hammingdistance.cpp -o hammingdistance.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c levenshteindistance.cpp -o levenshteindistance.o
levenshteindistance.cpp:41:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   41 |   unsigned int distances[n+1][m+1];
      |                               ^~~
levenshteindistance.cpp:41:31: note: read of non-const variable 'm' is not allowed in a constant expression
levenshteindistance.cpp:39:10: note: declared here
   39 |   size_t m = sequence.length();
      |          ^
levenshteindistance.cpp:41:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   41 |   unsigned int distances[n+1][m+1];
      |                          ^~~
levenshteindistance.cpp:41:26: note: function parameter 'n' with unknown value cannot be used in a constant expression
levenshteindistance.cpp:36:119: note: declared here
   36 | bool LevenshteinDistance::is_seq_insertable(const std::vector<Sequence> &seqs, const Sequence &sequence, const size_t n, const unsigned int min_dist) {
      |                                                                                                                       ^
levenshteindistance.cpp:102:33: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  102 |     unsigned int distances[n+1][m+1];
      |                                 ^~~
levenshteindistance.cpp:102:33: note: read of non-const variable 'm' is not allowed in a constant expression
levenshteindistance.cpp:99:12: note: declared here
   99 |     size_t m = read.length();
      |            ^
levenshteindistance.cpp:102:28: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  102 |     unsigned int distances[n+1][m+1];
      |                            ^~~
levenshteindistance.cpp:102:28: note: read of non-const variable 'n' is not allowed in a constant expression
levenshteindistance.cpp:84:10: note: declared here
   84 |   size_t n = barcodes[1].length();
      |          ^
levenshteindistance.cpp:155:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  155 |   unsigned int distances[n+1][n+1];
      |                               ^~~
levenshteindistance.cpp:155:31: note: function parameter 'n' with unknown value cannot be used in a constant expression
levenshteindistance.cpp:148:112: note: declared here
  148 | unsigned int LevenshteinDistance::static_min_set_distance(const std::vector<Sequence> &sequences, const size_t n, const unsigned int cost_sub, const unsigned int cost_indel) {
      |                                                                                                                ^
levenshteindistance.cpp:155:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  155 |   unsigned int distances[n+1][n+1];
      |                          ^~~
levenshteindistance.cpp:155:26: note: function parameter 'n' with unknown value cannot be used in a constant expression
levenshteindistance.cpp:148:112: note: declared here
  148 | unsigned int LevenshteinDistance::static_min_set_distance(const std::vector<Sequence> &sequences, const size_t n, const unsigned int cost_sub, const unsigned int cost_indel) {
      |                                                                                                                ^
levenshteindistance.cpp:200:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  200 |   unsigned int distances[n+1][m+1];
      |                               ^~~
levenshteindistance.cpp:200:31: note: read of non-const variable 'm' is not allowed in a constant expression
levenshteindistance.cpp:196:10: note: declared here
  196 |   size_t m = sequence.length();
      |          ^
levenshteindistance.cpp:200:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  200 |   unsigned int distances[n+1][m+1];
      |                          ^~~
levenshteindistance.cpp:200:26: note: function parameter 'n' with unknown value cannot be used in a constant expression
levenshteindistance.cpp:192:135: note: declared here
  192 | unsigned int LevenshteinDistance::static_min_seq_distance(const std::vector< Sequence > &seqs, const Sequence &sequence, const size_t n, const unsigned int cost_sub, const unsigned int cost_indel) {
      |                                                                                                                                       ^
levenshteindistance.cpp:239:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  239 |   unsigned int distances[n+1][m+1];
      |                               ^~~
levenshteindistance.cpp:239:31: note: read of non-const variable 'm' is not allowed in a constant expression
levenshteindistance.cpp:237:10: note: declared here
  237 |   size_t m = sequence2.length();
      |          ^
levenshteindistance.cpp:239:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  239 |   unsigned int distances[n+1][m+1];
      |                          ^~~
levenshteindistance.cpp:239:26: note: read of non-const variable 'n' is not allowed in a constant expression
levenshteindistance.cpp:236:10: note: declared here
  236 |   size_t n = sequence1.length();
      |          ^
10 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c phaseshiftdist.cpp -o phaseshiftdist.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c sequence.cpp -o sequence.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BH/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c sequencelevenshteindistance.cpp -o sequencelevenshteindistance.o
sequencelevenshteindistance.cpp:38:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   38 |   unsigned int distances[n+1][m+1];
      |                               ^~~
sequencelevenshteindistance.cpp:38:31: note: read of non-const variable 'm' is not allowed in a constant expression
sequencelevenshteindistance.cpp:34:10: note: declared here
   34 |   size_t m = sequence.length();
      |          ^
sequencelevenshteindistance.cpp:38:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   38 |   unsigned int distances[n+1][m+1];
      |                          ^~~
sequencelevenshteindistance.cpp:38:26: note: function parameter 'n' with unknown value cannot be used in a constant expression
sequencelevenshteindistance.cpp:33:127: note: declared here
   33 | bool SequenceLevenshteinDistance::is_seq_insertable(const std::vector<Sequence> &seqs, const Sequence &sequence, const size_t n, const unsigned int min_dist) {
      |                                                                                                                               ^
sequencelevenshteindistance.cpp:115:33: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  115 |     unsigned int distances[n+1][m+1];
      |                                 ^~~
sequencelevenshteindistance.cpp:115:33: note: read of non-const variable 'm' is not allowed in a constant expression
sequencelevenshteindistance.cpp:112:12: note: declared here
  112 |     size_t m = read.length();
      |            ^
sequencelevenshteindistance.cpp:115:28: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  115 |     unsigned int distances[n+1][m+1];
      |                            ^~~
sequencelevenshteindistance.cpp:115:28: note: read of non-const variable 'n' is not allowed in a constant expression
sequencelevenshteindistance.cpp:97:10: note: declared here
   97 |   size_t n = barcodes[1].length();
      |          ^
sequencelevenshteindistance.cpp:180:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  180 |   unsigned int distances[n+1][n+1];
      |                               ^~~
sequencelevenshteindistance.cpp:180:31: note: function parameter 'n' with unknown value cannot be used in a constant expression
sequencelevenshteindistance.cpp:175:120: note: declared here
  175 | unsigned int SequenceLevenshteinDistance::static_min_set_distance(const std::vector<Sequence> &sequences, const size_t n, const unsigned int cost_sub, const unsigned int cost_indel) {
      |                                                                                                                        ^
sequencelevenshteindistance.cpp:180:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  180 |   unsigned int distances[n+1][n+1];
      |                          ^~~
sequencelevenshteindistance.cpp:180:26: note: function parameter 'n' with unknown value cannot be used in a constant expression
sequencelevenshteindistance.cpp:175:120: note: declared here
  175 | unsigned int SequenceLevenshteinDistance::static_min_set_distance(const std::vector<Sequence> &sequences, const size_t n, const unsigned int cost_sub, const unsigned int cost_indel) {
      |                                                                                                                        ^
sequencelevenshteindistance.cpp:236:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  236 |   unsigned int distances[n+1][m+1];
      |                               ^~~
sequencelevenshteindistance.cpp:236:31: note: read of non-const variable 'm' is not allowed in a constant expression
sequencelevenshteindistance.cpp:230:10: note: declared here
  230 |   size_t m = sequence.length();
      |          ^
sequencelevenshteindistance.cpp:236:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  236 |   unsigned int distances[n+1][m+1];
      |                          ^~~
sequencelevenshteindistance.cpp:236:26: note: function parameter 'n' with unknown value cannot be used in a constant expression
sequencelevenshteindistance.cpp:229:141: note: declared here
  229 | unsigned int SequenceLevenshteinDistance::static_min_seq_distance(const std::vector<Sequence> &seqs, const Sequence &sequence, const size_t n, const unsigned int cost_sub, const unsigned int cost_indel) {
      |                                                                                                                                             ^
sequencelevenshteindistance.cpp:287:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  287 |   unsigned int distances[n+1][m+1];
      |                               ^~~
sequencelevenshteindistance.cpp:287:31: note: read of non-const variable 'm' is not allowed in a constant expression
sequencelevenshteindistance.cpp:285:10: note: declared here
  285 |   size_t m = sequence2.length();
      |          ^
sequencelevenshteindistance.cpp:287:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  287 |   unsigned int distances[n+1][m+1];
      |                          ^~~
sequencelevenshteindistance.cpp:287:26: note: read of non-const variable 'n' is not allowed in a constant expression
sequencelevenshteindistance.cpp:284:10: note: declared here
  284 |   size_t n = sequence1.length();
      |          ^
10 warnings generated.
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 DNABarcodeCompatibility.so DNABarcodes_init.o RcppExports.o cachedistance.o create_distance_func.o distance_for_R.o hammingdistance.o levenshteindistance.o phaseshiftdist.o sequence.o sequencelevenshteindistance.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.23-bioc/meat/DNABarcodeCompatibility.buildbin-libdir/00LOCK-DNABarcodeCompatibility/00new/DNABarcodeCompatibility/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (DNABarcodeCompatibility)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR DNABarcodeCompatibility.buildbin-libdir/DNABarcodeCompatibility/libs/DNABarcodeCompatibility.so
>>>>>>> 

>>>>>>> Paths before fix:
DNABarcodeCompatibility.buildbin-libdir/DNABarcodeCompatibility/libs/DNABarcodeCompatibility.so:
	DNABarcodeCompatibility.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!