################################################################################################################################################################## Running command:###### rm -rf mosbi.buildbin-libdir && mkdir mosbi.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh mosbi_1.16.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R mosbi.buildbin-libdir###############################################################################################################################################################>>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=mosbi.buildbin-libdir mosbi_1.16.0.tar.gz'>>>>>>> * installing *source* package ‘mosbi’ ...** this is package ‘mosbi’ version ‘1.16.0’** using staged installation** libsusing C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’using C++17using SDK: ‘MacOSX11.3.1.sdk’clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c attr_graph.cpp -o attr_graph.oattr_graph.cpp:123:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if((rownames(m)!=R_NilValue)&(colnames(m)!=R_NilValue)){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &&attr_graph.cpp:123:6: note: cast one or both operands to int to silence this warning1 warning generated.clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c attributeConnector.cpp -o attributeConnector.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c attribute_overlap.cpp -o attribute_overlap.oattribute_overlap.cpp:175:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if((rownames(occurance_m)!=R_NilValue)&(colnames(occurance_m)!=R_NilValue)){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &&attribute_overlap.cpp:175:6: note: cast one or both operands to int to silence this warning1 warning generated.clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bicluster_methods.cpp -o bicluster_methods.obicluster_methods.cpp:125:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical] if((row1.length()>row2.length())|(col1.length()>col2.length())){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ||bicluster_methods.cpp:125:6: note: cast one or both operands to int to silence this warningbicluster_methods.cpp:130:18: warning: loop variable 'i' of type 'const int &' binds to a temporary constructed from type 'typename storage_type<14>::type &' (aka 'double &') [-Wrange-loop-construct] for(const int& i : row1){ ^bicluster_methods.cpp:130:7: note: use non-reference type 'int' to make construction explicit or type 'const typename storage_type<14>::type &' (aka 'const double &') to prevent copying for(const int& i : row1){ ^~~~~~~~~~~~~~bicluster_methods.cpp:137:18: warning: loop variable 'j' of type 'const int &' binds to a temporary constructed from type 'typename storage_type<14>::type &' (aka 'double &') [-Wrange-loop-construct] for(const int& j : col1){ ^bicluster_methods.cpp:137:7: note: use non-reference type 'int' to make construction explicit or type 'const typename storage_type<14>::type &' (aka 'const double &') to prevent copying for(const int& j : col1){ ^~~~~~~~~~~~~~bicluster_methods.cpp:144:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if((irow==row1.length())&(irow==row2.length())& ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~bicluster_methods.cpp:144:6: note: cast one or both operands to int to silence this warningbicluster_methods.cpp:144:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if((irow==row1.length())&(irow==row2.length())& ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &&bicluster_methods.cpp:144:6: note: cast one or both operands to int to silence this warningbicluster_methods.cpp:144:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if((irow==row1.length())&(irow==row2.length())& ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &&bicluster_methods.cpp:144:6: note: cast one or both operands to int to silence this warningbicluster_methods.cpp:150:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if((irow==row1.length())&(icol==col1.length())){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &&bicluster_methods.cpp:150:6: note: cast one or both operands to int to silence this warningbicluster_methods.cpp:214:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if((!iinv(b, ereaseV))&(!iinv(b, identicalV))){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &&bicluster_methods.cpp:214:8: note: cast one or both operands to int to silence this warning8 warnings generated.clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost_graph.cpp -o boost_graph.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost_write.cpp -o boost_write.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c distance_matrix.cpp -o distance_matrix.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c extractBF.cpp -o extractBF.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c extractQUBIC2.cpp -o extractQUBIC2.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c full_graph.cpp -o full_graph.ofull_graph.cpp:111:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if((rownames(m)!=R_NilValue)&(colnames(m)!=R_NilValue)){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &&full_graph.cpp:111:6: note: cast one or both operands to int to silence this warning1 warning generated.clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c misc.cpp -o misc.omisc.cpp:20:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical] return(!((colnames(m)==R_NilValue)|(rownames(m)==R_NilValue))); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ||misc.cpp:20:12: note: cast one or both operands to int to silence this warning1 warning generated.clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c network_edge_strength.cpp -o network_edge_strength.onetwork_edge_strength.cpp:86:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] if((rownames(mat)!=R_NilValue)&(colnames(mat)!=R_NilValue)){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &&network_edge_strength.cpp:86:6: note: cast one or both operands to int to silence this warning1 warning generated.clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sample_biclusters.cpp -o sample_biclusters.oclang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c write_matrix.cpp -o write_matrix.oclang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o mosbi.so RcppExports.o attr_graph.o attributeConnector.o attribute_overlap.o bicluster_methods.o boost_graph.o boost_write.o distance_matrix.o extractBF.o extractQUBIC2.o full_graph.o misc.o network_edge_strength.o sample_biclusters.o write_matrix.o -L/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/lib -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework Rinstalling to /Users/biocbuild/bbs-3.22-bioc/meat/mosbi.buildbin-libdir/00LOCK-mosbi/00new/mosbi/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 (mosbi)>>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR mosbi.buildbin-libdir/mosbi/libs/mosbi.so>>>>>>> >>>>>>> Paths before fix:mosbi.buildbin-libdir/mosbi/libs/mosbi.so:mosbi.so (compatibility version 0.0.0, current version 0.0.0)@rpath/libtbb.dylib (compatibility version 0.0.0, current version 0.0.0)@rpath/libtbbmalloc.dylib (compatibility version 0.0.0, current version 0.0.0)/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.2)/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)>>>>>>> Fix with install_name_tool:install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "mosbi.buildbin-libdir/mosbi/libs/mosbi.so"install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "mosbi.buildbin-libdir/mosbi/libs/mosbi.so"install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "mosbi.buildbin-libdir/mosbi/libs/mosbi.so">>>>>>> Paths after fix:mosbi.buildbin-libdir/mosbi/libs/mosbi.so:mosbi.so (compatibility version 0.0.0, current version 0.0.0)@rpath/libtbb.dylib (compatibility version 0.0.0, current version 0.0.0)@rpath/libtbbmalloc.dylib (compatibility version 0.0.0, current version 0.0.0)/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.2)/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)