[BioC] RBGL installation on Ubuntu 6.10

[Li.Long at isb-sib.ch]

Hi,

I don't see the RBGL-version in quoted emails.

There was a bug in g++ 4.1 that is problematic in handling template(s), in
particular, "transitive_closure".  The codes are modified to work around
the problem at the end of May 2006.  You can read the comments in
    RBGL/src/transitive_closure.cpp
for more details (this file was created for the problem).

Let me know if the problem persists w/ work-around codes.

Li


> Thanks, the problem is solved! But now, I had the following error:
>
> * Installing *source* package 'RBGL' ...
> untarring boost include tree...
> ** libs
> g++ -I/usr/share/R/include -I/usr/share/R/include    -IboostIncl  -fpic
> -g
> -O2 -c bbc.cpp -o bbc.o
> g++ -I/usr/share/R/include -I/usr/share/R/include    -IboostIncl  -fpic
> -g
> -O2 -c cliques.cpp -o cliques.o
> g++ -I/usr/share/R/include -I/usr/share/R/include    -IboostIncl  -fpic
> -g
> -O2 -c hcs.cpp -o hcs.o
> g++ -I/usr/share/R/include -I/usr/share/R/include    -IboostIncl  -fpic
> -g
> -O2 -c incrConnComp.cpp -o incrConnComp.o
> g++ -I/usr/share/R/include -I/usr/share/R/include    -IboostIncl  -fpic
> -g
> -O2 -c interfaces.cpp -o interfaces.o
> boostIncl/boost/graph/depth_first_search.hpp: In function '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<unsigned int> >,
> std::allocator<std::vector<unsigned int, std::allocator<unsigned int> > >
> >,
> P =
> boost::topo_sort_visitor<std::back_insert_iterator<std::vector<unsigned
> int, std::allocator<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:   instantiated 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<unsigned int> >,
> std::allocator<std::vector<unsigned int, std::allocator<unsigned int> > >
> >,
> OutputIterator = std::back_insert_iterator<std::vector<unsigned int,
> std::allocator<unsigned int> > >, P = boost::identity_property_map, T =
> boost::vertex_index_t, R = boost::no_property]'
> boostIncl/boost/graph/transitive_closure.hpp:120:   instantiated 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<BGL_sequential_vertex_coloring::Vertex_Size_Type*,
> boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t,
> boost::default_color_type, boost::no_property>, unsigned int>, unsigned
> int,
> unsigned int&>, VertexIndexMap =
> boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t,
> boost::default_color_type, boost::no_property>, unsigned int>]'
> boostIncl/boost/graph/transitive_closure.hpp:263:   instantiated from
> 'void
> boost::transitive_closure(const Graph&, GraphTC&) [with Graph = Graph_dd,
> GraphTC = Graph_dd]'
> interfaces.cpp:371:   instantiated from here
> boostIncl/boost/graph/depth_first_search.hpp:324: error: no matching
> function for call to 'vertices(const std::vector<std::vector<unsigned int,
> std::allocator<unsigned int> >, std::allocator<std::vector<unsigned int,
> std::allocator<unsigned int> > > >&)'
> make: *** [interfaces.o] Error 1
> chmod: impossibile accedere a `/usr/local/lib/R/site-library/RBGL/libs/*':
> Nessun file o directory
> ERROR: compilation failed for package 'RBGL'
> ** Removing '/usr/local/lib/R/site-library/RBGL'
>
> I read in the mailing list about this error, but I didn't find the
> solution...
>
> Thank-you
>
> Davide
>
>
> 2006/11/29, lgautier at altern.org <lgautier at altern.org>:
>>
>> > Hello everyone,
>> >
>> > I tryed to install RBGL package on my linux ubuntu (v. 6.10 - Edgy ).
>> I
>> > found the following error:
>> >
>> > * Installing *source* package 'RBGL' ...
>> > untarring boost include tree...
>> > ** libs
>> > g++ -I/usr/share/R/include -I/usr/share/R/include    -IboostIncl
>> -fpic
>> > -g
>> > -O2 -c bbc.cpp -o bbc.o
>> > make: g++: Command not found
>> > make: *** [bbc.o] Error 127
>> > chmod: impossibile accedere a
>> `/usr/local/lib/R/site-library/RBGL/libs/*':
>> > Nessun file o directory
>> > ERROR: compilation failed for package 'RBGL'
>> > ** Removing '/usr/local/lib/R/site-library/RBGL'
>> >
>> > I installed g++ 4.1, lib g++ 2.8.1.3-dev, libboost-dev 1.33.1.
>> > Someone could help me?
>>
>> Ubuntu (as well as a number of other distributions) allow one to
>> have different versions of programs/libraries installed.
>>
>> Having the debian package g++-4.1 installed means that you have
>> an executable 'g++-4.1' in your path.
>> Having the debian package g++ installed will means you have the
>> default version installed (and 'g++' in your path). This is probably
>> want you want.
>>
>>
>> HTH,
>>
>>
>> L.
>>
>> >
>> > Thank-you very much
>> >
>> > Davide
>> >
>> >       [[alternative HTML version deleted]]
>> >
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>> >
>>
>>
>>
>
> 	[[alternative HTML version deleted]]
>
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