Package: CytoML

Version: 1.13.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CytoML

StartedAt: 2020-01-15 19:00:36 -0500 (Wed, 15 Jan 2020)

EndedAt: 2020-01-15 19:02:18 -0500 (Wed, 15 Jan 2020)

EllapsedTime: 101.9 seconds

RetCode: 0

Status:  OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CytoML
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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++ -std=gnu++11 accepts -g... yes
checking for gcc... clang
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang 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/usr/include/libxml2 -ftemplate-depth=900
configure:    PKG_LIBS=-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
clang++ -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/flowWorkspace/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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: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:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/H5CytoFrame.hpp:47:7: warning: 'cytolib::H5CytoFrame::set_params' hides overloaded virtual function [-Woverloaded-virtual]
        void set_params(const vector<cytoParam> & _params)
             ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:115:15: note: hidden overloaded virtual function 'cytolib::CytoFrame::set_params' declared here: different number of parameters (2 vs 1)
        virtual void set_params(const vector<cytoParam> & _params, bool force = false);
                     ^
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:433:30: warning: '/*' within block comment [-Wcomment]
           * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                                    ^
2 warnings generated.
clang++ -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -ftemplate-depth=900 -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/flowWorkspace/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/H5CytoFrame.hpp:47:7: warning: 'cytolib::H5CytoFrame::set_params' hides overloaded virtual function [-Woverloaded-virtual]
        void set_params(const vector<cytoParam> & _params)
             ^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib/include/cytolib/CytoFrame.hpp:115:15: note: hidden overloaded virtual function 'cytolib::CytoFrame::set_params' declared here: different number of parameters (2 vs 1)
        virtual void set_params(const vector<cytoParam> & _params, bool force = false);
                     ^
In file included from parseFlowJoWorkspace.cpp:9:
In file included from ../inst/include/CytoML/openWorkspace.hpp:12:
../inst/include/CytoML/winFlowJoWorkspace.hpp:433:30: warning: '/*' within block comment [-Wcomment]
           * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                                    ^
2 warnings generated.
clang++ -std=gnu++14 -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 -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-CytoML/00new/CytoML/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘ncdfFlow::filter’ by ‘dplyr::filter’ when loading ‘CytoML’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘ncdfFlow::filter’ by ‘dplyr::filter’ when loading ‘CytoML’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘ncdfFlow::filter’ by ‘dplyr::filter’ when loading ‘CytoML’
** testing if installed package keeps a record of temporary installation path
* DONE (CytoML)