[BioC] GOStats/RBGL installation error

[Nicolas Servant]

Hi,

1- RBGL_1.12.0.tar.gz form BioC2.0
2- CC: Sun C++ 5.8 Patch 121017-11 2007/05/02
This is the first time we use the Sun CC for R installation.
The last time we used the g++ compiler without any probleme.

Thanks
Nicolas

Li.Long at isb-sib.ch wrote:
> 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
>>
>>     
>
>
> .
>
>   


-- 
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/