##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL CytoML
###
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* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'CytoML' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
rm -f cpp11.o parseFlowJoWorkspace.o CytoML.dll
"F:/biocbuild/bbs-3.16-bioc/R/bin/x64/Rscript.exe" "../tools/winlibs.R" 2.9.10
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I../windows/libxml2-2.9.10/include/libxml2 -DLIBXML_STATIC -fpermissive -I'F:/biocbuild/bbs-3.16-bioc/R/library/cpp11/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cpp11.cpp -o cpp11.o
In file included from ../inst/include/CytoML/openWorkspace.hpp:12,
from CytoML_types.h:5,
from cpp11.cpp:4:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: "/*" within comment [-Wcomment]
435 | * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
|
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
194 | failed ************ (Pred::************
| ^
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/function.hpp:30,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
507 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
520 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
603 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
612 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
614 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/google/protobuf/io/coded_stream.h:135,
from F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include/cytolib/GatingSet.pb.h:23,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:6,
from CytoML_types.h:4,
from cpp11.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace/pairVectorCpp11Convert.h: In function 'cpp11::writable::doubles_matrix<> arma_to_rmatrix(const mat&)':
F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace/pairVectorCpp11Convert.h:33:21: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
33 | for (auto j = 0; j < m; j++) {
| ~~^~~
F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace/pairVectorCpp11Convert.h:34:22: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
34 | for (auto i = 0; i < n; i++) {
| ~~^~~
In file included from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from CytoML_types.h:5,
from cpp11.cpp:4:
../inst/include/CytoML/workspace_type.hpp: In function 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > CytoML::list_files(const string&, const string&)':
../inst/include/CytoML/workspace_type.hpp:67:124: warning: 'boost::filesystem::recursive_directory_iterator::recursive_directory_iterator(const boost::filesystem::path&, boost::filesystem::symlink_option)' is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations]
67 | for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse))
| ^
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/filesystem.hpp:18,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoVFS.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/global.hpp:21,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:5,
from CytoML_types.h:4,
from cpp11.cpp:4:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/filesystem/directory.hpp:577:5: note: declared here
577 | recursive_directory_iterator(path const& dir_path, BOOST_SCOPED_ENUM_NATIVE(symlink_option) opts)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from CytoML_types.h:5,
from cpp11.cpp:4:
../inst/include/CytoML/flowJoWorkspace.hpp: In member function 'std::unique_ptr<cytolib::GatingSet> CytoML::flowJoWorkspace::to_GatingSet(unsigned int, CytoML::ParseWorkspaceParameters, cytolib::GatingSet&)':
../inst/include/CytoML/flowJoWorkspace.hpp:201:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<CytoML::SampleInfo>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
201 | for (int i = 0; i < sample_infos.size(); i++)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from CytoML_types.h:5,
from cpp11.cpp:4:
../inst/include/CytoML/flowJoWorkspace.hpp: In member function 'std::vector<CytoML::SampleInfo> CytoML::flowJoWorkspace::get_sample_info(const std::vector<int, std::allocator<int> >&, const CytoML::ParseWorkspaceParameters&)':
../inst/include/CytoML/flowJoWorkspace.hpp:585:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
585 | for(int j = 0; j < sample_ids.size(); j++)
| ~~^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I../windows/libxml2-2.9.10/include/libxml2 -DLIBXML_STATIC -fpermissive -I'F:/biocbuild/bbs-3.16-bioc/R/library/cpp11/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c parseFlowJoWorkspace.cpp -o parseFlowJoWorkspace.o
In file included from ../inst/include/CytoML/openWorkspace.hpp:12,
from parseFlowJoWorkspace.cpp:10:
../inst/include/CytoML/winFlowJoWorkspace.hpp:435:30: warning: "/*" within comment [-Wcomment]
435 | * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
|
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
194 | failed ************ (Pred::************
| ^
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/function.hpp:30,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/transformation.hpp:18,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:15,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/cpp11/include/cpp11/as.hpp:5,
from F:/biocbuild/bbs-3.16-bioc/R/library/cpp11/include/cpp11.hpp:5,
from parseFlowJoWorkspace.cpp:9:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
58 | if(valVec.size() != 1+n+n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~
F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
62 | if(valVec.size() == 1+n+2*n*n){
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
68 | for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
../inst/include/CytoML/workspace_type.hpp: In function 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > > CytoML::list_files(const string&, const string&)':
../inst/include/CytoML/workspace_type.hpp:67:124: warning: 'boost::filesystem::recursive_directory_iterator::recursive_directory_iterator(const boost::filesystem::path&, boost::filesystem::symlink_option)' is deprecated: Use directory_options instead of symlink_option [-Wdeprecated-declarations]
67 | for(const fs::directory_entry & i: fs::recursive_directory_iterator(fs::path(data_dir), fs::symlink_option::recurse))
| ^
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/filesystem.hpp:18,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoVFS.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/global.hpp:21,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/compensation.hpp:19,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/CytoFrame.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/MemCytoFrame.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/gate.hpp:12,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/CytoML/wsNode.hpp:13,
from ../inst/include/CytoML/workspace_type.hpp:4,
from ../inst/include/CytoML/workspace.hpp:10,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/filesystem/directory.hpp:577:5: note: declared here
577 | recursive_directory_iterator(path const& dir_path, BOOST_SCOPED_ENUM_NATIVE(symlink_option) opts)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:22,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
74 | explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_SP_NOEXCEPT : px( p.release() )
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/cpp11/include/cpp11/as.hpp:5,
from F:/biocbuild/bbs-3.16-bioc/R/library/cpp11/include/cpp11.hpp:5,
from parseFlowJoWorkspace.cpp:9:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/cpp11/include/cpp11/as.hpp:5,
from F:/biocbuild/bbs-3.16-bioc/R/library/cpp11/include/cpp11.hpp:5,
from parseFlowJoWorkspace.cpp:9:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/cpp11/include/cpp11/as.hpp:5,
from F:/biocbuild/bbs-3.16-bioc/R/library/cpp11/include/cpp11.hpp:5,
from parseFlowJoWorkspace.cpp:9:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
507 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/cpp11/include/cpp11/as.hpp:5,
from F:/biocbuild/bbs-3.16-bioc/R/library/cpp11/include/cpp11.hpp:5,
from parseFlowJoWorkspace.cpp:9:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
520 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/cpp11/include/cpp11/as.hpp:5,
from F:/biocbuild/bbs-3.16-bioc/R/library/cpp11/include/cpp11.hpp:5,
from parseFlowJoWorkspace.cpp:9:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
603 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/cpp11/include/cpp11/as.hpp:5,
from F:/biocbuild/bbs-3.16-bioc/R/library/cpp11/include/cpp11.hpp:5,
from parseFlowJoWorkspace.cpp:9:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
612 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/cpp11/include/cpp11/as.hpp:5,
from F:/biocbuild/bbs-3.16-bioc/R/library/cpp11/include/cpp11.hpp:5,
from parseFlowJoWorkspace.cpp:9:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/property_map/property_map.hpp:598,
from F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:27,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/populationTree.hpp:14,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingHierarchy.hpp:17,
from F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/include/cytolib/GatingSet.hpp:14,
from ../inst/include/CytoML/workspace.hpp:14,
from ../inst/include/CytoML/flowJoWorkspace.hpp:11,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)':
F:/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
614 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\memory:83,
from F:/biocbuild/bbs-3.16-bioc/R/library/cpp11/include/cpp11/as.hpp:5,
from F:/biocbuild/bbs-3.16-bioc/R/library/cpp11/include/cpp11.hpp:5,
from parseFlowJoWorkspace.cpp:9:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.4.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
../inst/include/CytoML/flowJoWorkspace.hpp: In member function 'std::unique_ptr<cytolib::GatingSet> CytoML::flowJoWorkspace::to_GatingSet(unsigned int, CytoML::ParseWorkspaceParameters, cytolib::GatingSet&)':
../inst/include/CytoML/flowJoWorkspace.hpp:201:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<CytoML::SampleInfo>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
201 | for (int i = 0; i < sample_infos.size(); i++)
| ~~^~~~~~~~~~~~~~~~~~~~~
In file included from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
../inst/include/CytoML/flowJoWorkspace.hpp: In member function 'std::vector<CytoML::SampleInfo> CytoML::flowJoWorkspace::get_sample_info(const std::vector<int, std::allocator<int> >&, const CytoML::ParseWorkspaceParameters&)':
../inst/include/CytoML/flowJoWorkspace.hpp:585:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
585 | for(int j = 0; j < sample_ids.size(); j++)
| ~~^~~~~~~~~~~~~~~~~~~
In file included from F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace.h:6,
from parseFlowJoWorkspace.cpp:11:
F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace/pairVectorCpp11Convert.h: In function 'cpp11::writable::doubles_matrix<> arma_to_rmatrix(const mat&)':
F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace/pairVectorCpp11Convert.h:33:21: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
33 | for (auto j = 0; j < m; j++) {
| ~~^~~
F:/biocbuild/bbs-3.16-bioc/R/library/flowWorkspace/include/flowWorkspace/pairVectorCpp11Convert.h:34:22: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
34 | for (auto i = 0; i < n; i++) {
| ~~^~~
parseFlowJoWorkspace.cpp: In function 'cpp11::external_pointer<cytolib::GatingSet> parse_workspace(cpp11::external_pointer<CytoML::flowJoWorkspace>, int, cpp11::list, bool, std::string, cpp11::external_pointer<cytolib::GatingSet>, std::string, std::string, bool, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, bool, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, bool, bool, float, float, bool, bool, bool, bool, cpp11::list, bool, std::string, bool, SEXP, int)':
parseFlowJoWorkspace.cpp:103:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
103 | for(int i = 0; i < filter_names.size(); i++)
| ~~^~~~~~~~~~~~~~~~~~~~~
g++ -shared -s -static-libgcc -o CytoML.dll tmp.def cpp11.o parseFlowJoWorkspace.o -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -L../windows/libxml2-2.9.10/lib/x64-ucrt -lxml2 -llzma -liconv -lz F:/biocbuild/bbs-3.16-bioc/R/library/cytolib/lib/x64/libcytolib.a F:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/lib/x64/GatingSet.pb.o -LF:/biocbuild/bbs-3.16-bioc/R/library/RProtoBufLib/lib/x64 -lprotobuf -LF:/biocbuild/bbs-3.16-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LF:/biocbuild/bbs-3.16-bioc/R/library/Rhdf5lib/lib/x64-ucrt -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lsz -laec -lz -lpsapi -lws2_32 -lbcrypt -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-CytoML/00new/CytoML/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CytoML)
