[BioC] GOStats/RBGL installation error

[Li.Long at isb-sib.ch]

Hi,

First question: when and how you got the "RBGL"?
Second: what's your CC version?  Did you install RBGL with it successfully
before?  Or it's brandnew experience?  The error msgs are about C++
template handling.

Thanks

Li


> Hi,
>
> I try to install the GoStats (BioC 2.0, GoStat.2.2.6) package on R
> 2.5.1, but I have some C++ compilation errors due to RBGL package.
> The errors are link to the boost library and namespace definition.
> Does anybody have an idea ?
>
>
>  > sessionInfo()
> R version 2.5.1 (2007-06-27)
> sparc-sun-solaris2.9
>
> Error :
> * checking for file 'RBGL/DESCRIPTION' ... OK
> * preparing 'RBGL':
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> * running cleanup
> removing exploded boost header source...
> * installing the package to re-build vignettes
> * Installing *source* package 'RBGL' ...
> untarring boost include tree...
> ** libs
> /opt/SUNWspro/bin/CC -xO5 -xdepend -xlic_lib=sunperf -xmemalign=8s
> -xprefetch=auto,explicit -xtarget=native -lCstd
> -I/bioinfo/local/SunR/lib/R/include -I/bioinfo/local/SunR/lib/R/include
> -I/usr/local/include   -IboostIncl  -KPIC  -O -c bbc.cpp -o bbc.o
> CC: Warning: -O overwrites previously set optimization level of -O5
> CC: Warning: -xarch=native has been explicitly specified, or implicitly
> specified by a macro option, -xarch=native on this architecture implies
> -xarch=v8plusb which generates code that does not run on pre UltraSPARC
> III processors
> "boostIncl/boost/graph/betweenness_centrality.hpp", line 439: Error:
> Could not find a match for
> boost::make_iterator_property_map<boost::RAIter, boost::Value,
> boost::ID>(std::vector<boost::detail::edge_desc_impl<boost::undirected_tag,
> unsigned> >*,
> ........
> boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t,
> int, boost::property<boost::vertex_centrality_t, double,
> boost::no_property>>, unsigned>).
> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493:     Where:
> While instantiating
> "boost::detail::graph::brandes_betweenness_centrality_dispatch2<boost::adjacency_list<boost::vecS,
>
> ........
>  boost::property<boost::vertex_centrality_t, double,
> boost::no_property>>, unsigned>)".
> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493:     Where:
> Instantiated from
> boost::brandes_betweenness_centrality<boost::adjacency_list<boost::vecS,
> boost::vecS,
> .........
>  boost::vertex_centrality_t>, boost::vertex_centrality_t,
> boost::no_property>>>&).
> "bbc.cpp", line 43:     Where: Instantiated from non-template code.
> "boostIncl/boost/graph/betweenness_centrality.hpp", line 440: Error:
> Could not find a match for
> boost::make_iterator_property_map<boost::RAIter, boost::Value,
> boost::ID>(double*,
> ..........
>  boost::property<boost::vertex_centrality_t, double,
> boost::no_property>>, unsigned>)".
> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493:     Where:
> Instantiated from
> boost::brandes_betweenness_centrality<boost::adjacency_list<boost::vecS,
> boost::vecS,
> ............
> boost::vertex_centrality_t>, boost::vertex_centrality_t,
> boost::no_property>>>&).
> "bbc.cpp", line 43:     Where: Instantiated from non-template code.
> ..............
> "boostIncl/boost/graph/betweenness_centrality.hpp", line 441: Error:
> Could not find a match for
> boost::make_iterator_property_map<boost::RAIter, boost::Value,
> boost::ID>(double*,  boost::property<boost::vertex_centrality_t, double,
> boost::no_property>>, unsigned>)".
> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493:     Where:
> Instantiated from
> boost::brandes_betweenness_centrality<boost::adjacency_list<boost::vecS,
> boost::vecS,
> ..............
>  boost::vertex_centrality_t>, boost::vertex_centrality_t,
> boost::no_property>>>&).
> "bbc.cpp", line 43:     Where: Instantiated from non-template code.
> "boostIncl/boost/graph/betweenness_centrality.hpp", line 442: Error:
> Could not find a match for
> boost::make_iterator_property_map<boost::RAIter, boost::Value,
> boost::ID>(unsigned*,
> ..................
>  boost::property<boost::vertex_centrality_t, double,
> boost::no_property>>, unsigned>)".
> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493:     Where:
> Instantiated from
> boost::brandes_betweenness_centrality<boost::adjacency_list<boost::vecS,
> boost::vecS,
> .............
>  boost::vertex_centrality_t>, boost::vertex_centrality_t,
> boost::no_property>>>&).
> "bbc.cpp", line 43:     Where: Instantiated from non-template code.
> 4 Error(s) detected.
> make: *** [bbc.o] Error 4
>
>
> Thanks for your help,
> Regards,
>
> Nicolas.
>
>
> --
> Nicolas Servant
> Equipe Bioinformatique
> Institut Curie
> 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE
>
> Email: Nicolas.Servant at curie.fr
> Tel: 01 53 10 70 55
> http://bioinfo.curie.fr/
>
> _______________________________________________
> 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
>