################################################################################################################################################################## Running command:###### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CytoML###############################################################################################################################################################* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’* installing *source* package ‘CytoML’ ...** this is package ‘CytoML’ version ‘2.22.0’** using staged installationchecking whether the C++ compiler works... yeschecking for C++ compiler default output file name... a.outchecking for suffix of executables... checking whether we are cross compiling... nochecking for suffix of object files... ochecking whether we are using the GNU C++ compiler... yeschecking whether clang++ -arch x86_64 -std=gnu++11 accepts -g... yeschecking for gcc... clang -arch x86_64checking whether we are using the GNU C compiler... yeschecking whether clang -arch x86_64 accepts -g... yeschecking for clang -arch x86_64 option to accept ISO C89... none neededconfigure: setting xml2 flags...configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods.checking for xml2-config... /usr/bin/xml2-configconfigure: setting cytolib-ml commandline tool path...configure: Using the following compilation and linking flagsconfigure: PKG_CPPFLAGS=-I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -ftemplate-depth=900configure: PKG_LIBS=-L/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm configure: CYTOLIBML_BIN=/usr/local/binconfigure: creating ./config.statusconfig.status: creating src/Makevarsconfig.status: creating R/cytolibml_bin_path.R** libsusing C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’using C++11using SDK: ‘MacOSX11.3.1.sdk’clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -ftemplate-depth=900 -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/flowWorkspace/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cpp11.cpp -o cpp11.oIn file included from cpp11.cpp:4:In file included from ./CytoML_types.h:4:In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/flowWorkspace/include/flowWorkspace.h:5:In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14:In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17:In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13:In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:/Library/Frameworks/R.framework/Versions/4.5-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/4.5-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 ./CytoML_types.h:5:In file included from ../inst/include/CytoML/openWorkspace.hpp:11:In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10:In file included from ../inst/include/CytoML/flowJoWorkspace.hpp:11:In file included from ../inst/include/CytoML/workspace.hpp:10:In file included from ../inst/include/CytoML/workspace_type.hpp:4:../inst/include/CytoML/wsNode.hpp:27:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] Rprintf("%.*s", n, s); ~~^~ ~In file included from cpp11.cpp:4:In file included from ./CytoML_types.h:5:In file included from ../inst/include/CytoML/openWorkspace.hpp:12:../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: '/*' within block comment [-Wcomment] * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate ^3 warnings generated.clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -ftemplate-depth=900 -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/flowWorkspace/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.oIn file included from parseFlowJoWorkspace.cpp:10:In file included from ../inst/include/CytoML/openWorkspace.hpp:11:In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10:In file included from ../inst/include/CytoML/flowJoWorkspace.hpp:11:In file included from ../inst/include/CytoML/workspace.hpp:10:In file included from ../inst/include/CytoML/workspace_type.hpp:4:In file included from ../inst/include/CytoML/wsNode.hpp:13:In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13:In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14:/Library/Frameworks/R.framework/Versions/4.5-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/4.5-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 parseFlowJoWorkspace.cpp:10:In file included from ../inst/include/CytoML/openWorkspace.hpp:11:In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10:In file included from ../inst/include/CytoML/flowJoWorkspace.hpp:11:In file included from ../inst/include/CytoML/workspace.hpp:10:In file included from ../inst/include/CytoML/workspace_type.hpp:4:../inst/include/CytoML/wsNode.hpp:27:20: warning: field precision should have type 'int', but argument has type 'std::streamsize' (aka 'long') [-Wformat] Rprintf("%.*s", n, s); ~~^~ ~In file included from parseFlowJoWorkspace.cpp:10:In file included from ../inst/include/CytoML/openWorkspace.hpp:12:../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: '/*' within block comment [-Wcomment] * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate ^3 warnings generated.clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o CytoML.so cpp11.o parseFlowJoWorkspace.o /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/cytolib/lib/libcytolib.a /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.5-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 -L/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework Rinstalling to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-CytoML/00new/CytoML/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 (CytoML)