############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowWorkspace_4.12.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R flowWorkspace.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=flowWorkspace.buildbin-libdir flowWorkspace_4.12.2.tar.gz' >>>>>>> * installing *source* package ‘flowWorkspace’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_API.cpp -o R_API.o In file included from R_API.cpp:9: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct] for (const pb::Range range : gate_pb.mrg().ranges()) { ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying for (const pb::Range range : gate_pb.mrg().ranges()) { ^~~~~~~~~~~~~~~~~~~~~~~ & 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o In file included from R_GatingHierarchy.cpp:18: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct] for (const pb::Range range : gate_pb.mrg().ranges()) { ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying for (const pb::Range range : gate_pb.mrg().ranges()) { ^~~~~~~~~~~~~~~~~~~~~~~ & 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_GatingSet.cpp -o R_GatingSet.o In file included from R_GatingSet.cpp:10: In file included from ./flowWorkspace_types.h:8: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct] for (const pb::Range range : gate_pb.mrg().ranges()) { ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying for (const pb::Range range : gate_pb.mrg().ranges()) { ^~~~~~~~~~~~~~~~~~~~~~~ & 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cpp11.cpp -o cpp11.o In file included from cpp11.cpp:4: In file included from ./flowWorkspace_types.h:8: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct] for (const pb::Range range : gate_pb.mrg().ranges()) { ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying for (const pb::Range range : gate_pb.mrg().ranges()) { ^~~~~~~~~~~~~~~~~~~~~~~ & In file included from cpp11.cpp:4: In file included from ./flowWorkspace_types.h:5: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include/cpp11/declarations.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include/cpp11.hpp:10: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include/cpp11/external_pointer.hpp:17:3: warning: delete called on non-final 'cytolib::CytoFrameView' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete obj; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include/cpp11/external_pointer.hpp:20:42: note: in instantiation of function template specialization 'cpp11::default_deleter' requested here template > ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cytoframeAPI.cpp -o cytoframeAPI.o In file included from cytoframeAPI.cpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct] for (const pb::Range range : gate_pb.mrg().ranges()) { ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying for (const pb::Range range : gate_pb.mrg().ranges()) { ^~~~~~~~~~~~~~~~~~~~~~~ & In file included from cytoframeAPI.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include/cpp11.hpp:10: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include/cpp11/external_pointer.hpp:17:3: warning: delete called on non-final 'cytolib::CytoFrameView' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete obj; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include/cpp11/external_pointer.hpp:20:42: note: in instantiation of function template specialization 'cpp11::default_deleter' requested here template > ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cytosetAPI.cpp -o cytosetAPI.o In file included from cytosetAPI.cpp:2: In file included from ../inst/include/flowWorkspace/pairVectorCpp11Convert.h:12: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct] for (const pb::Range range : gate_pb.mrg().ranges()) { ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying for (const pb::Range range : gate_pb.mrg().ranges()) { ^~~~~~~~~~~~~~~~~~~~~~~ & In file included from cytosetAPI.cpp:2: In file included from ../inst/include/flowWorkspace/pairVectorCpp11Convert.h:10: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include/cpp11.hpp:10: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include/cpp11/external_pointer.hpp:17:3: warning: delete called on non-final 'cytolib::CytoFrameView' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor] delete obj; ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include/cpp11/external_pointer.hpp:20:42: note: in instantiation of function template specialization 'cpp11::default_deleter' requested here template > ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c getDescendants.cpp -o getDescendants.o In file included from getDescendants.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct] for (const pb::Range range : gate_pb.mrg().ranges()) { ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying for (const pb::Range range : gate_pb.mrg().ranges()) { ^~~~~~~~~~~~~~~~~~~~~~~ & 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c getPopStats.cpp -o getPopStats.o In file included from getPopStats.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct] for (const pb::Range range : gate_pb.mrg().ranges()) { ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying for (const pb::Range range : gate_pb.mrg().ranges()) { ^~~~~~~~~~~~~~~~~~~~~~~ & 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c getSingleCellExpression.cpp -o getSingleCellExpression.o In file included from getSingleCellExpression.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct] for (const pb::Range range : gate_pb.mrg().ranges()) { ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying for (const pb::Range range : gate_pb.mrg().ranges()) { ^~~~~~~~~~~~~~~~~~~~~~~ & 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c h5_error_r_handler.cpp -o h5_error_r_handler.o In file included from h5_error_r_handler.cpp:8: In file included from ../inst/include/flowWorkspace/pairVectorCpp11Convert.h:12: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct] for (const pb::Range range : gate_pb.mrg().ranges()) { ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying for (const pb::Range range : gate_pb.mrg().ranges()) { ^~~~~~~~~~~~~~~~~~~~~~~ & 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c setCounts.cpp -o setCounts.o In file included from setCounts.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:26: warning: loop variable 'range' creates a copy from type 'const pb::Range' [-Wrange-loop-construct] for (const pb::Range range : gate_pb.mrg().ranges()) { ^ /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/include/cytolib/gate.hpp:238:10: note: use reference type 'const pb::Range &' to prevent copying for (const pb::Range range : gate_pb.mrg().ranges()) { ^~~~~~~~~~~~~~~~~~~~~~~ & 1 warning generated. clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o flowWorkspace.so R_API.o R_GatingHierarchy.o R_GatingSet.o cpp11.o cytoframeAPI.o cytosetAPI.o getDescendants.o getPopStats.o getSingleCellExpression.o h5_error_r_handler.o setCounts.o /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/cytolib/lib/libcytolib.a /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.17-bioc/meat/flowWorkspace.buildbin-libdir/00LOCK-flowWorkspace/00new/flowWorkspace/libs ** R ** 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 (flowWorkspace) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR flowWorkspace.buildbin-libdir/flowWorkspace/libs/flowWorkspace.so >>>>>>> >>>>>>> Paths before fix: flowWorkspace.buildbin-libdir/flowWorkspace/libs/flowWorkspace.so: flowWorkspace.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.1) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgcc_s.1.1.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/flowWorkspace.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/flowWorkspace.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs/flowWorkspace.so" >>>>>>> Paths after fix: flowWorkspace.buildbin-libdir/flowWorkspace/libs/flowWorkspace.so: flowWorkspace.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.1) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)