############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CytoML ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * 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++ -mmacosx-version-min=10.13 -std=gnu++11 accepts -g... yes checking for gcc... clang -mmacosx-version-min=10.13 checking whether we are using the GNU C compiler... yes checking whether clang -mmacosx-version-min=10.13 accepts -g... yes checking for clang -mmacosx-version-min=10.13 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/local/opt/libxml2/bin/xml2-config configure: setting cytolib-ml commandline tool path... configure: Using the following compilation and linking flags configure: PKG_CPPFLAGS=-I/usr/local/Cellar/libxml2/2.9.10_2/include/libxml2 -ftemplate-depth=900 configure: PKG_LIBS=-L/usr/local/Cellar/libxml2/2.9.10_2/lib -lxml2 -lz -lpthread -liconv -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 clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/local/Cellar/libxml2/2.9.10_2/include/libxml2 -ftemplate-depth=900 -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/flowWorkspace/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from ./../inst/include/CytoML.h:4: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/flowWorkspace/include/flowWorkspace.h:5: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cytolib/include/cytolib/populationTree.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use instead. [-W#pragma-messages] BOOST_HEADER_DEPRECATED("") ^ /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED' # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") ^ /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :108:2: note: expanded from here message("This header is deprecated. Use " "" " instead.") ^ In file included from RcppExports.cpp:4: In file included from ./../inst/include/CytoML.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 ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/local/Cellar/libxml2/2.9.10_2/include/libxml2 -ftemplate-depth=900 -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/flowWorkspace/include' -I/usr/local/include -fPIC -Wall -g -O2 -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o In file included from parseFlowJoWorkspace.cpp:9: 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:14: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cytolib/include/cytolib/GatingSet.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cytolib/include/cytolib/GatingHierarchy.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cytolib/include/cytolib/populationTree.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_list.hpp:255: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/detail/adjacency_list.hpp:37: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/graph/adjacency_iterator.hpp:13: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/detail/iterator.hpp:13:1: warning: This header is deprecated. Use instead. [-W#pragma-messages] BOOST_HEADER_DEPRECATED("") ^ /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED' # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") ^ /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ :12:2: note: expanded from here message("This header is deprecated. Use " "" " instead.") ^ In file included from parseFlowJoWorkspace.cpp:9: 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 ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -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/usr/local/lib -o CytoML.so RcppExports.o parseFlowJoWorkspace.o /Library/Frameworks/R.framework/Versions/4.1/Resources/library/cytolib/lib/libcytolib.a /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/lib/libsz.a -lz -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/Cellar/libxml2/2.9.10_2/lib -lxml2 -lz -lpthread -liconv -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/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)