RBGL installation on Ubuntu 6.10
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@bagatti-davide-1946
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@lgautieralternorg-747
Last seen 7.4 years ago
> 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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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<unsig ned=""> 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_colo r_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_colo r_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]] >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at stat.math.ethz.ch >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> >> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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