[BioC] deprecated head file for RBGL and compilation failure
eastasiax [guest]
guest at bioconductor.org
Sun Apr 15 10:05:07 CEST 2012
please update qt header file to version 4.8 or greater. there were many warnings while compiling. here are some:
* installing *source* package ‘RBGL’ ...
untarring boost include tree...
** libs
g++ -I/usr/include/R/ -DNDEBUG -I/usr/local/include -IboostIncl -fpic -march=i686 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -c bbc.cpp -o bbc.o
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
from boostIncl/boost/graph/adjacency_list.hpp:25,
from RBGL.hpp:26,
from bbc.cpp:1:
/usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
g++ -I/usr/include/R/ -DNDEBUG -I/usr/local/include -IboostIncl -fpic -march=i686 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -c cliques.cpp -o cliques.o
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
from boostIncl/boost/graph/adjacency_list.hpp:25,
from RBGL.hpp:26,
from cliques.cpp:1:
/usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
g++ -I/usr/include/R/ -DNDEBUG -I/usr/local/include -IboostIncl -fpic -march=i686 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -c clusteringCoef.cpp -o clusteringCoef.o
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
from boostIncl/boost/graph/adjacency_list.hpp:25,
from RBGL.hpp:26,
from clusteringCoef.cpp:1:
/usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
g++ -I/usr/include/R/ -DNDEBUG -I/usr/local/include -IboostIncl -fpic -march=i686 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -c dominatorTree.cpp -o dominatorTree.o
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
from boostIncl/boost/graph/adjacency_list.hpp:25,
from RBGL.hpp:26,
from dominatorTree.cpp:1:
/usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
g++ -I/usr/include/R/ -DNDEBUG -I/usr/local/include -IboostIncl -fpic -march=i686 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
from boostIncl/boost/graph/adjacency_list.hpp:25,
from RBGL.hpp:26,
from edmonds_optimum_branching.cpp:1:
/usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
g++ -I/usr/include/R/ -DNDEBUG -I/usr/local/include -IboostIncl -fpic -march=i686 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -c hcs.cpp -o hcs.o
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
from boostIncl/boost/graph/adjacency_list.hpp:25,
from RBGL.hpp:26,
from hcs.cpp:1:
/usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
g++ -I/usr/include/R/ -DNDEBUG -I/usr/local/include -IboostIncl -fpic -march=i686 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -c incrConnComp.cpp -o incrConnComp.o
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
from boostIncl/boost/graph/adjacency_list.hpp:25,
from RBGL.hpp:26,
from incrConnComp.cpp:1:
/usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
g++ -I/usr/include/R/ -DNDEBUG -I/usr/local/include -IboostIncl -fpic -march=i686 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -c interfaces.cpp -o interfaces.o
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
from boostIncl/boost/graph/adjacency_list.hpp:25,
from RBGL.hpp:26,
from interfaces.cpp:1:
/usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
g++ -I/usr/include/R/ -DNDEBUG -I/usr/local/include -IboostIncl -fpic -march=i686 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -c layout.cpp -o layout.o
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
from boostIncl/boost/graph/adjacency_list.hpp:25,
from RBGL.hpp:26,
from layout.cpp:1:
/usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
g++ -I/usr/include/R/ -DNDEBUG -I/usr/local/include -IboostIncl -fpic -march=i686 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -c minST.cpp -o minST.o
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
from boostIncl/boost/graph/adjacency_list.hpp:25,
from RBGL.hpp:26,
from minST.cpp:1:
/usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
g++ -I/usr/include/R/ -DNDEBUG -I/usr/local/include -IboostIncl -fpic -march=i686 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -c mincut.cpp -o mincut.o
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
from boostIncl/boost/graph/adjacency_list.hpp:25,
from RBGL.hpp:26,
from mincut.cpp:1:
/usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
g++ -I/usr/include/R/ -DNDEBUG -I/usr/local/include -IboostIncl -fpic -march=i686 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -c ordering.cpp -o ordering.o
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
from boostIncl/boost/graph/adjacency_list.hpp:25,
from RBGL.hpp:26,
from ordering.cpp:1:
/usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
g++ -I/usr/include/R/ -DNDEBUG -I/usr/local/include -IboostIncl -fpic -march=i686 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -c planar.cpp -o planar.o
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
from boostIncl/boost/graph/adjacency_list.hpp:25,
from RBGL.hpp:26,
from planar.cpp:1:
/usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
g++ -I/usr/include/R/ -DNDEBUG -I/usr/local/include -IboostIncl -fpic -march=i686 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -c shortestPath.cpp -o shortestPath.o
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
from boostIncl/boost/graph/adjacency_list.hpp:25,
from RBGL.hpp:26,
from shortestPath.cpp:1:
/usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
g++ -I/usr/include/R/ -DNDEBUG -I/usr/local/include -IboostIncl -fpic -march=i686 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -c sna.cpp -o sna.o
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
from boostIncl/boost/graph/adjacency_list.hpp:25,
from RBGL.hpp:26,
from sna.cpp:1:
/usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
g++ -I/usr/include/R/ -DNDEBUG -I/usr/local/include -IboostIncl -fpic -march=i686 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -c transitive_closure.cpp -o transitive_closure.o
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/hash_set:61:0,
from boostIncl/boost/graph/adjacency_list.hpp:25,
from RBGL.hpp:26,
from transitive_closure.cpp:16:
/usr/lib/gcc/i686-pc-linux-gnu/4.7.0/../../../../include/c++/4.7.0/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
some errors caused interrupt of compilation process.
In file included from boostIncl/boost/graph/detail/adjacency_list.hpp:30:0,
from boostIncl/boost/graph/adjacency_list.hpp:313,
from RBGL.hpp:26,
from transitive_closure.cpp:16:
boostIncl/boost/graph/graph_concepts.hpp: In instantiation of ‘boost::concepts::IncidenceGraph<G>::~IncidenceGraph() [with G = std::vector<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >]’:
boostIncl/boost/graph/graph_concepts.hpp:70:1: required from ‘static void boost::concept::requirement<Model>::failed() [with Model = boost::concepts::IncidenceGraphConcept<std::vector<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > > >]’
boostIncl/boost/concept_check.hpp:43:1: required from ‘void boost::function_requires(Model*) [with Model = boost::concepts::IncidenceGraphConcept<std::vector<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > > >]’
boostIncl/boost/graph/depth_first_search.hpp:84:7: required from ‘void boost::detail::depth_first_visit_impl(const IncidenceGraph&, typename boost::graph_traits<Graph>::vertex_descriptor, DFSVisitor&, ColorMap, TerminatorFunc) [with IncidenceGraph = std::vector<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >; DFSVisitor = boost::topo_sort_visitor<std::back_insert_iterator<std::vector<unsigned int> > >; ColorMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<boost::default_color_type*, std::vector<boost::default_color_type> >, boost::identity_property_map, boost::default_color_type, boost::default_color_type&>; TerminatorFunc = boost::detail::nontruth2; typename boost::graph_traits<Graph>::vertex_descriptor = unsigned int]’
boostIncl/boost/graph/depth_first_search.hpp:201:7: required from ‘void boost::depth_first_search(const VertexListGraph&, DFSVisitor, ColorMap, typename boost::graph_traits<Graph>::vertex_descriptor) [with VertexListGraph = std::vector<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >; DFSVisitor = boost::topo_sort_visitor<std::back_insert_iterator<std::vector<unsigned int> > >; ColorMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<boost::default_color_type*, std::vector<boost::default_color_type> >, boost::identity_property_map, boost::default_color_type, boost::default_color_type&>; typename boost::graph_traits<Graph>::vertex_descriptor = unsigned int]’
boostIncl/boost/graph/depth_first_search.hpp:249:9: required from ‘static void boost::detail::dfs_dispatch<boost::detail::error_property_not_found>::apply(const VertexListGraph&, DFSVisitor, Vertex, const boost::bgl_named_params<P, T, R>&, boost::detail::error_property_not_found) [with VertexListGraph = std::vector<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >; Vertex = unsigned int; DFSVisitor = boost::topo_sort_visitor<std::back_insert_iterator<std::vector<unsigned int> > >; P = boost::topo_sort_visitor<std::back_insert_iterator<std::vector<unsigned int> > >; T = boost::graph_visitor_t; R = boost::bgl_named_params<boost::identity_property_map, boost::vertex_index_t, boost::no_property>]’
boostIncl/boost/graph/depth_first_search.hpp:329:5: required from ‘void boost::depth_first_search(const VertexListGraph&, const boost::bgl_named_params<P, T, R>&) [with VertexListGraph = std::vector<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >; P = boost::topo_sort_visitor<std::back_insert_iterator<std::vector<unsigned int> > >; T = boost::graph_visitor_t; R = boost::bgl_named_params<boost::identity_property_map, boost::vertex_index_t, boost::no_property>]’
boostIncl/boost/graph/topological_sort.hpp:64:5: required from ‘void boost::topological_sort(VertexListGraph&, OutputIterator, const boost::bgl_named_params<P, T, R>&) [with VertexListGraph = std::vector<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >; OutputIterator = std::back_insert_iterator<std::vector<unsigned int> >; P = boost::identity_property_map; T = boost::vertex_index_t; R = boost::no_property]’
boostIncl/boost/graph/transitive_closure.hpp:120:5: required from ‘void boost::transitive_closure(const Graph&, GraphTC&, G_to_TC_VertexMap, VertexIndexMap) [with Graph = R_adjacency_list<boost::directedS, double>; GraphTC = R_adjacency_list<boost::directedS, double>; G_to_TC_VertexMap = boost::iterator_property_map<unsigned int*, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, unsigned int>, unsigned int, unsigned int&>; VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, unsigned int>]’
boostIncl/boost/graph/transitive_closure.hpp:263:5: required from ‘void boost::transitive_closure(const Graph&, GraphTC&) [with Graph = R_adjacency_list<boost::directedS, double>; GraphTC = R_adjacency_list<boost::directedS, double>]’
transitive_closure.cpp:29:30: required from here
boostIncl/boost/graph/graph_concepts.hpp:88:11: error: ‘out_edges’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
In file included from boostIncl/boost/graph/transpose_graph.hpp:16:0,
from boostIncl/boost/graph/strong_components.hpp:258,
from boostIncl/boost/graph/transitive_closure.hpp:18,
from transitive_closure.cpp:17:
boostIncl/boost/graph/reverse_graph.hpp:151:1: note: ‘template<class BidirectionalGraph, class GRef> std::pair<typename boost::graph_traits<Graph>::in_edge_iterator, typename boost::graph_traits<Graph>::in_edge_iterator> boost::out_edges(typename boost::graph_traits<Graph>::vertex_descriptor, const boost::reverse_graph<Graph, GraphRef>&)’ declared here, later in the translation unit
In file included from boostIncl/boost/graph/detail/adjacency_list.hpp:30:0,
from boostIncl/boost/graph/adjacency_list.hpp:313,
from RBGL.hpp:26,
from transitive_closure.cpp:16:
boostIncl/boost/graph/graph_concepts.hpp:89:11: error: ‘out_degree’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
In file included from boostIncl/boost/graph/transpose_graph.hpp:16:0,
from boostIncl/boost/graph/strong_components.hpp:258,
from boostIncl/boost/graph/transitive_closure.hpp:18,
from transitive_closure.cpp:17:
boostIncl/boost/graph/reverse_graph.hpp:173:1: note: ‘template<class BidirectionalGraph, class GRef> typename boost::graph_traits<Graph>::degree_size_type boost::out_degree(typename boost::graph_traits<Graph>::vertex_descriptor, const boost::reverse_graph<Graph, GraphRef>&)’ declared here, later in the translation unit
make: *** [transitive_closure.o] Error 1
ERROR: compilation failed for package ‘RBGL’
* removing ‘/home/neoanima/.Rlib/RBGL’
The downloaded source packages are in
‘/tmp/RtmpOs7NUf/downloaded_packages’
Warning message:
In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘RBGL’ had non-zero exit status
please fix them.
-- output of sessionInfo():
R>sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: i686-pc-linux-gnu (32-bit)
locale:
[1] LC_CTYPE=zh_CN.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=C
[5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] BiocInstaller_1.4.3 MASS_7.3-17
loaded via a namespace (and not attached):
[1] tools_2.15.0
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