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###
### Running command:
###
###   rm -rf HiCDCPlus.buildbin-libdir && mkdir HiCDCPlus.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh HiCDCPlus_1.19.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R HiCDCPlus.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=HiCDCPlus.buildbin-libdir HiCDCPlus_1.19.0.tar.gz'
>>>>>>> 

* installing *source* package ‘HiCDCPlus’ ...
** this is package ‘HiCDCPlus’ version ‘1.19.0’
** using staged installation
** libs
specified C++11
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
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/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/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c straw.cpp -o straw.o
straw.cpp:330:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  330 |   char compressedBytes[idx.size];
      |                        ^~~~~~~~
straw.cpp:330:24: note: read of non-constexpr variable 'idx' is not allowed in a constant expression
straw.cpp:325:14: note: declared here
  325 |   indexEntry idx = blockMap[blockNumber];
      |              ^
straw.cpp:459:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  459 |   char buffer[entry.size];
      |               ^~~~~~~~~~
straw.cpp:459:15: note: function parameter 'entry' with unknown value cannot be used in a constant expression
straw.cpp:458:66: note: declared here
  458 | vector<double> readNormalizationVector(ifstream& fin, indexEntry entry) {
      |                                                                  ^
2 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 HiCDCPlus.so RcppExports.o straw.o -lz -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.23-bioc/meat/HiCDCPlus.buildbin-libdir/00LOCK-HiCDCPlus/00new/HiCDCPlus/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (HiCDCPlus)


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

>>>>>>> Paths before fix:
HiCDCPlus.buildbin-libdir/HiCDCPlus/libs/HiCDCPlus.so:
	HiCDCPlus.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.12)
	/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!