############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CytoML ### ############################################################################## ############################################################################## * checking for file ‘CytoML/DESCRIPTION’ ... OK * preparing ‘CytoML’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package ‘CytoML’ ... ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether clang++ -arch x86_64 -std=gnu++11 accepts -g... yes checking for gcc... clang -arch x86_64 checking whether we are using the GNU C compiler... yes checking whether clang -arch x86_64 accepts -g... yes checking for clang -arch x86_64 option to accept ISO C89... none needed configure: 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-config configure: setting cytolib-ml commandline tool path... configure: Using the following compilation and linking flags configure: PKG_CPPFLAGS=-I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -ftemplate-depth=900 configure: PKG_LIBS=-L/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm configure: CYTOLIBML_BIN=/usr/local/bin configure: creating ./config.status config.status: creating src/Makevars config.status: creating R/cytolibml_bin_path.R ** 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/ -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include -ftemplate-depth=900 -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cpp11/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/flowWorkspace/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 ./CytoML_types.h:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/flowWorkspace/include/flowWorkspace.h:5: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/populationTree.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/nodeProperties.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/cytolib/include/cytolib/POPINDICES.hpp:14: /Library/Frameworks/R.framework/Versions/4.4-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/4.4-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: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: ../inst/include/CytoML/workspace_type.hpp:67:101: error: no member named 'symlink_option' in namespace 'boost::filesystem' for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse)) ~~~~^ 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 and 1 error generated. make: *** [cpp11.o] Error 1 ERROR: compilation failed for package ‘CytoML’ * removing ‘/private/tmp/RtmpS5z9Uz/Rinst173b04f47c0dc/CytoML’ ----------------------------------- ERROR: package installation failed