[BioC] 'citation("RBGL")' command produces package not found error
Jeremiah Willcock
jewillco at osl.iu.edu
Thu May 24 19:24:04 CEST 2012
On Thu, 24 May 2012, Dan Tenenbaum wrote:
> Hi Jeremiah,
>
> On Thu, May 24, 2012 at 10:13 AM, Jeremiah Willcock <jewillco at osl.iu.edu> wrote:
>> I am not an expert user of R, and I am looking to get the citation for the
>> RBGL package. I am using R 2.15.0,
>
> If you are using R 2.15 you should be using Bioconductor 2.10, and
> therefore looking at this page:
>
> http://bioconductor.org/packages/2.10/bioc/html/RBGL.html
I switched to that later; the install directions and first part of the
demo file are the same, though.
> and I entered the two commands on
>> http://bioc.ism.ac.jp/2.8/bioc/html/RBGL.html to install RBGL. I was not
>> running as root, so R created a subdirectory under my home directory for the
>> installation. RBGL appeared to install successfully, but when I try to get
>> the citation, I get:
>>
>>> citation("RBGL")
>>
>> Error in citation("RBGL") : package ‘RBGL’ not found
>>
>> Trying to run 'library(RBGL)' (the first non-comment line in the demo file
>> at http://bioc.ism.ac.jp/2.8/bioc/vignettes/RBGL/inst/doc/RBGL.R) produces:
>>
>>> library(RBGL)
>>
>> Error in library(RBGL) : there is no package called ‘RBGL’
>>
>> What steps should I take to make sure the package is installed correctly?
>
>
> What was the output of:
>
> source("http://bioconductor.org/biocLite.R")
> biocLite("RBGL")
I should have checked that more carefully -- it failed to compile (with
g++ 4.7.0). Here's the last part of the error message:
In file included from boostIncl/boost/graph/detail/adjacency_list.hpp:30:0,
from boostIncl/boost/graph/adjacency_list.hpp:313,
from RBGL.hpp:26,
from transitive_closure.cpp:16:
boostIncl/boost/graph/graph_concepts.hpp: In instantiation of ‘boost::concepts::IncidenceGraph<G>::~IncidenceGraph() [with G = std::vector<std::vector<long unsigned int>, std::allocator<std::vector<long unsigned int> > >]’:
boostIncl/boost/graph/graph_concepts.hpp:70:1: required from ‘static void boost::concept::requirement<Model>::failed() [with Model = boost::concepts::IncidenceGraphConcept<std::vector<std::vector<long unsigned int>, std::allocator<std::vector<long unsigned int> > > >]’
boostIncl/boost/concept_check.hpp:43:1: required from ‘void boost::function_requires(Model*) [with Model = boost::concepts::IncidenceGraphConcept<std::vector<std::vector<long unsigned int>, std::allocator<std::vector<long unsigned int> > > >]’
boostIncl/boost/graph/depth_first_search.hpp:84:7: required from ‘void boost::detail::depth_first_visit_impl(const IncidenceGraph&, typename boost::graph_traits<Graph>::vertex_descriptor, DFSVisitor&, ColorMap, TerminatorFunc) [with IncidenceGraph = std::vector<std::vector<long unsigned int>, std::allocator<std::vector<long unsigned int> > >; DFSVisitor = boost::topo_sort_visitor<std::back_insert_iterator<std::vector<long unsigned int> > >; ColorMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<boost::default_color_type*, std::vector<boost::default_color_type> >, boost::identity_property_map, boost::default_color_type, boost::default_color_type&>; TerminatorFunc = boost::detail::nontruth2; typename boost::graph_traits<Graph>::vertex_descriptor = long unsigned int]’
boostIncl/boost/graph/depth_first_search.hpp:201:7: required from ‘void boost::depth_first_search(const VertexListGraph&, DFSVisitor, ColorMap, typename boost::graph_traits<Graph>::vertex_descriptor) [with VertexListGraph = std::vector<std::vector<long unsigned int>, std::allocator<std::vector<long unsigned int> > >; DFSVisitor = boost::topo_sort_visitor<std::back_insert_iterator<std::vector<long unsigned int> > >; ColorMap = boost::iterator_property_map<__gnu_cxx::__normal_iterator<boost::default_color_type*, std::vector<boost::default_color_type> >, boost::identity_property_map, boost::default_color_type, boost::default_color_type&>; typename boost::graph_traits<Graph>::vertex_descriptor = long unsigned int]’
boostIncl/boost/graph/depth_first_search.hpp:249:9: required from ‘static void boost::detail::dfs_dispatch<boost::detail::error_property_not_found>::apply(const VertexListGraph&, DFSVisitor, Vertex, const boost::bgl_named_params<P, T, R>&, boost::detail::error_property_not_found) [with VertexListGraph = std::vector<std::vector<long unsigned int>, std::allocator<std::vector<long unsigned int> > >; Vertex = long unsigned int; DFSVisitor = boost::topo_sort_visitor<std::back_insert_iterator<std::vector<long unsigned int> > >; P = boost::topo_sort_visitor<std::back_insert_iterator<std::vector<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/depth_first_search.hpp:329:5: required from ‘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<std::vector<long unsigned int> > >; P = boost::topo_sort_visitor<std::back_insert_iterator<std::vector<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:64:5: required 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<std::vector<long unsigned int> > >; OutputIterator = std::back_insert_iterator<std::vector<long unsigned int> >; P = boost::identity_property_map; T = boost::vertex_index_t; R = boost::no_property]’
boostIncl/boost/graph/transitive_closure.hpp:120:5: required 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<long unsigned int*, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, 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>, long unsigned int>]’
boostIncl/boost/graph/transitive_closure.hpp:263:5: required from ‘void boost::transitive_closure(const Graph&, GraphTC&) [with Graph = R_adjacency_list<boost::directedS, double>; GraphTC = R_adjacency_list<boost::directedS, double>]’
transitive_closure.cpp:29:30: required from here
boostIncl/boost/graph/graph_concepts.hpp:88:11: error: ‘out_edges’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
In file included from boostIncl/boost/graph/transpose_graph.hpp:16:0,
from boostIncl/boost/graph/strong_components.hpp:258,
from boostIncl/boost/graph/transitive_closure.hpp:18,
from transitive_closure.cpp:17:
boostIncl/boost/graph/reverse_graph.hpp:151:1: note: ‘template<class BidirectionalGraph, class GRef> std::pair<typename boost::graph_traits<Graph>::in_edge_iterator, typename boost::graph_traits<Graph>::in_edge_iterator> boost::out_edges(typename boost::graph_traits<Graph>::vertex_descriptor, const boost::reverse_graph<Graph, GraphRef>&)’ declared here, later in the translation unit
In file included from boostIncl/boost/graph/detail/adjacency_list.hpp:30:0,
from boostIncl/boost/graph/adjacency_list.hpp:313,
from RBGL.hpp:26,
from transitive_closure.cpp:16:
boostIncl/boost/graph/graph_concepts.hpp:89:11: error: ‘out_degree’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
In file included from boostIncl/boost/graph/transpose_graph.hpp:16:0,
from boostIncl/boost/graph/strong_components.hpp:258,
from boostIncl/boost/graph/transitive_closure.hpp:18,
from transitive_closure.cpp:17:
boostIncl/boost/graph/reverse_graph.hpp:173:1: note: ‘template<class BidirectionalGraph, class GRef> typename boost::graph_traits<Graph>::degree_size_type boost::out_degree(typename boost::graph_traits<Graph>::vertex_descriptor, const boost::reverse_graph<Graph, GraphRef>&)’ declared here, later in the translation unit
make: *** [transitive_closure.o] Error 1
ERROR: compilation failed for package ‘RBGL’
* removing ‘/nfs/deep-thought/home/users/jewillco/R/x86_64-redhat-linux-gnu-library/2.15/RBGL’
The downloaded source packages are in
‘/tmp/Rtmp28G8jD/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘RBGL’ had non-zero exit status
2: installed directory not writable, cannot update packages 'foreign', 'MASS',
'mgcv', 'msm', 'mvtnorm', 'nlme', 'RODBC', 'survival', 'zoo', 'car',
'multcomp', 'systemfit'
I think a lot of the warnings are from using an old version of BGL;
newer ones have many bug fixes applied and warnings resolved.
> Also, what is the output of
> sessionInfo()
> ?
R version 2.15.0 (2012-03-30)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
>
>
>> Could someone please send me (or post) the citation, without needing to
>> install the package to access it? Thank you.
>
>> citation("RBGL")
>
> To cite package ‘RBGL’ in publications use:
>
> Vince Carey, Li Long and R. Gentleman (). RBGL: An interface to the
> BOOST graph library. R package version 1.31.1.
> http://www.bioconductor.org
>
> A BibTeX entry for LaTeX users is
>
> @Manual{,
> title = {RBGL: An interface to the BOOST graph library},
> author = {Vince Carey and Li Long and R. Gentleman},
> note = {R package version 1.31.1},
> url = {http://www.bioconductor.org},
> }
>
> ATTENTION: This citation information has been auto-generated from the
> package DESCRIPTION file and may need manual editing, see
> ‘help("citation")’ .
>
> Warning message:
> In citation("RBGL") : no date field in DESCRIPTION file of package ‘RBGL’
Thank you very much for that.
-- Jeremiah Willcock
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