############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf R3CPET.buildbin-libdir && mkdir R3CPET.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh R3CPET_1.28.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R R3CPET.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=R3CPET.buildbin-libdir R3CPET_1.28.0.tar.gz' >>>>>>> * installing *source* package ‘R3CPET’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c R3CPET_init.c -o R3CPET_init.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c corpus.cpp -o corpus.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c main.cpp -o main.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c state.cpp -o state.o state.cpp:171:7: warning: 'random_shuffle >' is deprecated [-Wdeprecated-declarations] std::random_shuffle ( doc_states_.begin(), doc_states_.end() ); ^ /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/algorithm:2982:1: note: 'random_shuffle >' has been explicitly marked deprecated here _LIBCPP_DEPRECATED_IN_CXX14 void ^ /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1107:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX14' # define _LIBCPP_DEPRECATED_IN_CXX14 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ state.cpp:173:12: warning: 'random_shuffle >' is deprecated [-Wdeprecated-declarations] std::random_shuffle ( doc_states_[j]->words_.begin(), doc_states_[j]->words_.end() ); ^ /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/algorithm:2982:1: note: 'random_shuffle >' has been explicitly marked deprecated here _LIBCPP_DEPRECATED_IN_CXX14 void ^ /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1107:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX14' # define _LIBCPP_DEPRECATED_IN_CXX14 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c stirln.cpp -o stirln.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -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++ -mmacosx-version-min=10.13 -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/usr/local/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 installing to /Users/biocbuild/bbs-3.15-bioc/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 "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "R3CPET.buildbin-libdir/R3CPET/libs/R3CPET.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "R3CPET.buildbin-libdir/R3CPET/libs/R3CPET.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "R3CPET.buildbin-libdir/R3CPET/libs/R3CPET.so"