[BioC] RBGL 1.8.1 installation error on linux

[Francois Pepin]

On Thu, 2006-05-11 at 09:46 -0700, rgentlem wrote:
> Hi,
> 
> Johannes Rainer wrote:
> > hi,
> > 
> > thanks robert for your help.
> > based on your suggestions i tested now some new settings, i used the gcc 
> > 3.2.3 compiler (g++32 ) to compile the package (unfortunately there is 
> 
> Hmm,
>   I don't think that is the right set of numbers for a gcc compiler,
>   4.0.3 and 3.4.5 are the up to date versions are reported at:
>   http://gcc.gnu.org/.
> 
>   I don't know why there would not be a version of all for FC5, 
> certainly there were discussions of it and some of the early work on FC5 
> was based on the 4.0 arm (4.1 is very new, released 2006-02-28). You 
> should be able to build these from source if you wanted to.
> 
>    I remain convinced that these are likely compiler bugs and hence 
> someone at Redhat or gcc might care, we are not really able to do much 
> about them. Sorry we don't have such a beast here for any testing so I 
> cannot say much more that would be helpful.
>   best wishes
>     Robert

I have the same setup as Johannes (FC5 on amd64), and I'm getting
exactly the same error.

The full output is show below, there are around 5 errors in there.

> getBioC('RBGL')
Running getBioC version 0.1.6 with R version 2.3.0
Running biocinstall version 1.8.2 with R version 2.3.0
Your version of R requires version 1.8 of Bioconductor.
trying URL
'http://bioconductor.org/packages/1.8/bioc/src/contrib/RBGL_1.8.1.tar.gz'
Content type 'application/x-gzip' length 1460061 bytes
opened URL
==================================================
downloaded 1425Kb

* Installing *source* package 'RBGL' ...
untarring boost include tree...
** libs
g++ -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include  -
I/usr/local/include  -IboostIncl  -fpic  -g -O2 -c bbc.cpp -o bbc.o
g++ -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include  -
I/usr/local/include  -IboostIncl  -fpic  -g -O2 -c cliques.cpp -o
cliques.o
g++ -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include  -
I/usr/local/include  -IboostIncl  -fpic  -g -O2 -c hcs.cpp -o hcs.o
g++ -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include  -
I/usr/local/include  -IboostIncl  -fpic  -g -O2 -c incrConnComp.cpp -o
incrConnComp.o
g++ -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include  -
I/usr/local/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<long unsigned int, std::allocator<long unsigned
int> >, std::allocator<std::vector<long unsigned int,
std::allocator<long unsigned int> > > >, P =
boost::topo_sort_visitor<std::back_insert_iterator<std::vector<long
unsigned int, std::allocator<long 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<long unsigned int, std::allocator<long unsigned
int> >, std::allocator<std::vector<long unsigned int,
std::allocator<long unsigned int> > > >, OutputIterator =
std::back_insert_iterator<std::vector<long unsigned int,
std::allocator<long 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>, long unsigned int>, long unsigned int, long unsigned int&>, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type, boost::no_property>, long 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<long
unsigned int, std::allocator<long unsigned int> >,
std::allocator<std::vector<long unsigned int, std::allocator<long
unsigned int> > > >&)’
make: *** [interfaces.o] Error 1
chmod: cannot access `/usr/local/lib64/R/library/RBGL/libs/*': No such
file or directory
ERROR: compilation failed for package 'RBGL'
** Removing '/usr/local/lib64/R/library/RBGL


> sessionInfo()
Version 2.3.0 (2006-04-24)
x86_64-unknown-linux-gnu

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"
"datasets"
[7] "base"


[francois at flims tmp]$ gcc --version
gcc (GCC) 4.1.0 20060304 (Red Hat 4.1.0-3)