Error while executing Make

[fredericokremer]

Does any one know what the following error my represent, and how do i fixt it? i'm using the latest version of Boost, and trying to run Bridger in a Ubuntu server 13.10.

./lemon/topology.h:1215:34: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs]
     typedef typename Graph::Edge Edge;
                                  ^
./lemon/topology.h: In function 'bool lemon::bipartite(const UGraph&)':
./lemon/topology.h:1470:37: warning: typedef 'EdgeIt' locally defined but not used [-Wunused-local-typedefs]
     typedef typename UGraph::EdgeIt EdgeIt;
                                     ^
./lemon/topology.h: In function 'bool lemon::bipartitePartitions(const UGraph&, NodeMap&)':
./lemon/topology.h:1514:35: warning: typedef 'Node' locally defined but not used [-Wunused-local-typedefs]
     typedef typename UGraph::Node Node;
                                   ^
./lemon/topology.h:1516:37: warning: typedef 'EdgeIt' locally defined but not used [-Wunused-local-typedefs]
     typedef typename UGraph::EdgeIt EdgeIt;
                                     ^
In file included from reachability_bp_graph.h:45:0,
                 from reachability_bp_graph.cpp:13:
transitive_closure.h: In function 'void get_transitive_closure(const Graph&, GraphTC&, G_to_TC_VertexMap, VertexIndexMap)':
transitive_closure.h:76:60: warning: typedef 'edge' locally defined but not used [-Wunused-local-typedefs]
   typedef typename graph_traits < Graph >::edge_descriptor edge;
                                                            ^
transitive_closure.h:194:64: warning: typedef 'tc_vertex' locally defined but not used [-Wunused-local-typedefs]
   typedef typename graph_traits < GraphTC >::vertex_descriptor tc_vertex;
                                                                ^
transitive_closure.h: In function 'void warshall_transitive_closure(G&)':
transitive_closure.h:281:58: warning: typedef 'vertex' locally defined but not used [-Wunused-local-typedefs]
   typedef typename graph_traits < G >::vertex_descriptor vertex;
                                                          ^
transitive_closure.h: In function 'void warren_transitive_closure(G&)':
transitive_closure.h:304:58: warning: typedef 'vertex' locally defined but not used [-Wunused-local-typedefs]
   typedef typename graph_traits < G >::vertex_descriptor vertex;
                                                          ^
In file included from ./lemon/list_graph.h:26:0,
                 from ./lemon/dfs.h:26,
                 from ./lemon/topology.h:22,
                 from reachability_bp_graph.h:22,
                 from reachability_bp_graph.cpp:13:
./lemon/bits/base_extender.h: In instantiation of 'lemon::BidirBpUGraphExtender<Base>::Node lemon::BidirBpUGraphExtender<Base>::source(const UEdge&) const [with Base = lemon::SmartBpUGraphBase; lemon::BidirBpUGraphExtender<Base>::Node = lemon::SmartBpUGraphBase::Node; lemon::BidirBpUGraphExtender<Base>::UEdge = lemon::SmartBpUGraphBase::UEdge]':
reachability_bp_graph.cpp:81:70:   required from here
./lemon/bits/base_extender.h:362:21: error: 'aNode' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
    return aNode(edge);
                     ^
./lemon/bits/base_extender.h:362:21: note: declarations in dependent base 'lemon::SmartBpUGraphBase' are not found by unqualified lookup
./lemon/bits/base_extender.h:362:21: note: use 'this->aNode' instead
./lemon/bits/base_extender.h: In instantiation of 'lemon::BidirBpUGraphExtender<Base>::Node lemon::BidirBpUGraphExtender<Base>::target(const UEdge&) const [with Base = lemon::SmartBpUGraphBase; lemon::BidirBpUGraphExtender<Base>::Node = lemon::SmartBpUGraphBase::Node; lemon::BidirBpUGraphExtender<Base>::UEdge = lemon::SmartBpUGraphBase::UEdge]':
reachability_bp_graph.cpp:82:70:   required from here
./lemon/bits/base_extender.h:365:21: error: 'bNode' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
    return bNode(edge);
                     ^
./lemon/bits/base_extender.h:365:21: note: declarations in dependent base 'lemon::SmartBpUGraphBase' are not found by unqualified lookup
./lemon/bits/base_extender.h:365:21: note: use 'this->bNode' instead
make[2]: *** [PathSearch-reachability_bp_graph.o] Error 1
make[2]: Leaving directory `/home/cdtec/Frederico/programas/Bridger_r2014-11-05/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/cdtec/Frederico/programas/Bridger_r2014-11-05'
make: *** [all] Error 2

[EvolbioMainz]

Hello, I'd like to report the same problem. We'll continue working on it tomorrow, I'll report back if there is any success.

[EvolbioMainz]

So we have it running now. This download is not the version that worked for us. Use this instead: https://sourceforge.net/projects/rnaseqassembly/

Before executing "make", go and edit src/assemble.cpp : comment out the line (errAbort(const_cast<char*>("Cannot create directory % !\n"), out_dir.c_str()))

with "//" and then make Bridger. Good luck.

EDIT In the end we will be using Velvet or keep the poor Trinity assembly we have. Bridger is still not working, the older version is not giving us a puzzling error. So anyway, good luck to all who follow.