##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CytoML
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 g++ -std=gnu++11 accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc 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: Using the following compilation and linking flags
configure: PKG_CPPFLAGS=-I/usr/include/libxml2
configure: PKG_LIBS=-lxml2
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DROUT -I../inst/include/ -I/usr/include/libxml2 -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppParallel/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/flowWorkspace/openWorkspace.hpp:12:0,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
../inst/include/flowWorkspace/winFlowJoWorkspace.hpp:433:30: warning: "/*" within comment [-Wcomment]
* "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function.hpp:30,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template T * get_pointer(std::auto_ptr const& p)
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 0; i < x.size(); i++){
~~^~~~~~~~~~
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 0; i < nEvents; i++)
~~^~~~~~~~~
In file included from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11:0,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
../inst/include/flowWorkspace/workspace.hpp: In member function ‘void workspace::toArray(std::__cxx11::string, std::vector&, std::vector&)’:
../inst/include/flowWorkspace/workspace.hpp:108:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned i=0;i class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/graph/adj_list_serialize.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:18,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/function.hpp:30,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from /home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:24,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template T * get_pointer(std::auto_ptr const& p)
^~~~~~~~
In file included from /usr/include/c++/7/memory:80:0,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/global.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/spline.hpp:12,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/calibrationTable.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/transformation.hpp:23,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/gate.hpp:14,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:15,
from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/nodeProperties.hpp:11:0,
from ../inst/include/flowWorkspace/wsNode.hpp:10,
from ../inst/include/flowWorkspace/workspace.hpp:14,
from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector BOOLINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:103:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 0; i < x.size(); i++){
~~^~~~~~~~~~
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp: In member function ‘virtual std::vector ROOTINDICES::getIndices_u()’:
/home/biocbuild/bbs-3.9-bioc/R/library/cytolib/include/cytolib/POPINDICES.hpp:228:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 0; i < nEvents; i++)
~~^~~~~~~~~
In file included from ../inst/include/flowWorkspace/flowJoWorkspace.hpp:11:0,
from ../inst/include/flowWorkspace/macFlowJoWorkspace.hpp:10,
from ../inst/include/flowWorkspace/openWorkspace.hpp:11,
from parseFlowJoWorkspace.cpp:10:
../inst/include/flowWorkspace/workspace.hpp: In member function ‘void workspace::toArray(std::__cxx11::string, std::vector&, std::vector&)’:
../inst/include/flowWorkspace/workspace.hpp:108:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned i=0;i
