[BioC] GOStats/RBGL installation error

[Nicolas Servant]

Hi Tony,

I'm sorry, but for now, we cannot update the R and BioC versions.
R is installed on a sparc-sun-solaris server for all our applications. 
And it's always complicated, for all developers and application users, 
to make this type of update.
Moreover, i'm not convinced that it could resolve the probleme ...

Thanks for your help,
Best,
Nicolas

Tony Chiang wrote:
> Hi Nicolas,
>
> Can you try and update your R to 2.6 and your Bioc to 2.2 to see if this
> problem still persists?
> Or is there a reason you are using the old versions of R and Bioc?
>
> Best,
> --Tony
>
> On 10/26/07, Nicolas Servant <Nicolas.Servant at curie.fr> wrote:
>   
>> 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/
>>
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>>
>>     
>
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>   


-- 
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/