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###
### Running command:
###
###   rm -rf R3CPET.buildbin-libdir && mkdir R3CPET.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh R3CPET_1.31.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R R3CPET.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=R3CPET.buildbin-libdir R3CPET_1.31.0.tar.gz'
>>>>>>> 

* installing *source* package ‘R3CPET’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX13.0.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R3CPET_init.c -o R3CPET_init.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/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++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c corpus.cpp -o corpus.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c main.cpp -o main.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c state.cpp -o state.o
state.cpp:171:7: warning: 'random_shuffle<std::__wrap_iter<DocState **>>' is deprecated [-Wdeprecated-declarations]
        std::random_shuffle ( doc_states_.begin(), doc_states_.end() ); 
             ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/shuffle.h:60:1: note: 'random_shuffle<std::__wrap_iter<DocState **>>' has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX14 void
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1060:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX14'
#  define _LIBCPP_DEPRECATED_IN_CXX14 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
state.cpp:173:12: warning: 'random_shuffle<std::__wrap_iter<WordInfo *>>' is deprecated [-Wdeprecated-declarations]
      std::random_shuffle ( doc_states_[j]->words_.begin(), doc_states_[j]->words_.end() );
           ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/shuffle.h:60:1: note: 'random_shuffle<std::__wrap_iter<WordInfo *>>' has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX14 void
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1060:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX14'
#  define _LIBCPP_DEPRECATED_IN_CXX14 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c stirln.cpp -o stirln.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utils.cpp -o utils.o
utils.cpp:5:14: warning: unused variable 'half_ln_2pi' [-Wunused-const-variable]
const double half_ln_2pi = 0.91893853320467267;
             ^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o R3CPET.so R3CPET_init.o RcppExports.o corpus.o main.o state.o stirln.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/R3CPET.buildbin-libdir/00LOCK-R3CPET/00new/R3CPET/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
NOTE: arguments in definition for validity method for class 'ChromMaintainers' changed from (x) to (object)
NOTE: arguments in definition for validity method for class 'HLDAResult' changed from (x) to (object)
NOTE: arguments in definition for validity method for class 'NetworkCollection' changed from (x) to (object)
** 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 (R3CPET)


>>>>>>> 
>>>>>>> FIXING LINKS FOR R3CPET.buildbin-libdir/R3CPET/libs/R3CPET.so
>>>>>>> 

install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "R3CPET.buildbin-libdir/R3CPET/libs/R3CPET.so"
install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "R3CPET.buildbin-libdir/R3CPET/libs/R3CPET.so"
install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "R3CPET.buildbin-libdir/R3CPET/libs/R3CPET.so"