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BioC 2.13: CHECK report for RBGL on zin1

This page was generated on 2014-04-05 09:47:02 -0700 (Sat, 05 Apr 2014).

Package 574/750HostnameOS / ArchBUILDCHECKBUILD BIN
RBGL 1.38.0
Bioconductor Package Maintainer
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/RBGL
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: RBGL
Version: 1.38.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings RBGL_1.38.0.tar.gz
StartedAt: 2014-04-05 03:22:19 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 03:24:17 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 117.7 seconds
RetCode: 0
Status:  OK 
CheckDir: RBGL.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/RBGL.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RBGL/DESCRIPTION’ ... OK
* this is package ‘RBGL’ version ‘1.38.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RBGL’ can be installed ... [84s/86s] OK
* checking installed package size ... NOTE
  installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
‘library’ or ‘require’ call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘RBGL.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [3s/3s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/RBGL.Rcheck/00check.log’
for details.

RBGL.Rcheck/00install.out:

* installing *source* package ‘RBGL’ ...
untarring boost include tree...
** libs
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c bbc.cpp -o bbc.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c cliques.cpp -o cliques.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c clusteringCoef.cpp -o clusteringCoef.o
clusteringCoef.cpp: In function ‘SEXPREC* graphGenerator(SEXP, SEXP, SEXP)’:
clusteringCoef.cpp:394:40: warning: ‘u’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c dominatorTree.cpp -o dominatorTree.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c hcs.cpp -o hcs.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c incrConnComp.cpp -o incrConnComp.o
incrConnComp.cpp: In function ‘SEXPREC* BGL_incr_comp_internal(SEXP, SEXP, SEXP, E_IC_METHOD)’:
incrConnComp.cpp:74:6: warning: unused variable ‘child_index’ [-Wunused-variable]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c interfaces.cpp -o interfaces.o
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c minST.cpp -o minST.o
In file included from minST.cpp:2:0:
rbgl_trimmed_boost_1_49_0/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘void boost::detail::kruskal_mst_impl(const Graph&, OutputIterator, Rank, Parent, Weight) [with Graph = R_adjacency_list<boost::directedS, double>, OutputIterator = std::back_insert_iterator<std::vector<boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > >, Rank = boost::iterator_property_map<__gnu_cxx::__normal_iterator<long unsigned int*, std::vector<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&>, Parent = boost::iterator_property_map<__gnu_cxx::__normal_iterator<long unsigned int*, std::vector<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&>, Weight = boost::adj_list_edge_property_map<boost::directed_tag, double, const double&, long unsigned int, const boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>]’:
rbgl_trimmed_boost_1_49_0/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)(& ei)+48).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::<anonymous>.boost::iterator_adaptor<boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>, __gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, boost::use_default, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_iterator.__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >::_M_current’ may be used uninitialized in this function [-Wuninitialized]
rbgl_trimmed_boost_1_49_0/boost/graph/kruskal_min_spanning_tree.hpp:78:51: note: ‘*((void*)(& ei)+48).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::<anonymous>.boost::iterator_adaptor<boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>, __gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, boost::use_default, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_iterator.__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >::_M_current’ was declared here
rbgl_trimmed_boost_1_49_0/boost/graph/detail/edge.hpp:29:34: warning: ‘*((void*)(& ei)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_src’ may be used uninitialized in this function [-Wuninitialized]
rbgl_trimmed_boost_1_49_0/boost/graph/kruskal_min_spanning_tree.hpp:78:51: note: ‘*((void*)(& ei)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_src’ was declared here
rbgl_trimmed_boost_1_49_0/boost/graph/kruskal_min_spanning_tree.hpp:48:5: warning: ‘*((void*)(& ei)+32).__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >::_M_current’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c mincut.cpp -o mincut.o
rbgl_trimmed_boost_1_49_0/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘SEXPREC* BGL_max_flow_internal(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, E_MF_METHOD)’:
rbgl_trimmed_boost_1_49_0/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)(& ei)+48).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::<anonymous>.boost::iterator_adaptor<boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>, __gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > > > > >, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, boost::use_default, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_iterator.__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > > > > >::_M_current’ may be used uninitialized in this function [-Wuninitialized]
mincut.cpp:99:19: note: ‘*((void*)(& ei)+48).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::<anonymous>.boost::iterator_adaptor<boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>, __gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > > > > >, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, boost::use_default, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_iterator.__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > > > > >::_M_current’ was declared here
mincut.cpp:103:54: warning: ‘*((void*)(& ei)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_capacity_t, double, boost::property<boost::edge_residual_capacity_t, double, boost::property<boost::edge_reverse_t, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int> > > > > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_src’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c ordering.cpp -o ordering.o
ordering.cpp: In function ‘SEXPREC* BGL_king_ordering(SEXP, SEXP, SEXP, SEXP)’:
ordering.cpp:180:48: warning: variable ‘id’ set but not used [-Wunused-but-set-variable]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c planar.cpp -o planar.o
planar.cpp: In function ‘SEXPREC* planarFaceTraversal(SEXP, SEXP, SEXP)’:
planar.cpp:161:50: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
planar.cpp:165:58: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
planar.cpp: In function ‘SEXPREC* planarCanonicalOrdering(SEXP, SEXP, SEXP)’:
planar.cpp:256:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
planar.cpp:225:34: warning: variable ‘oi_end’ set but not used [-Wunused-but-set-variable]
planar.cpp: In function ‘SEXPREC* isStraightLineDrawing(SEXP, SEXP, SEXP, SEXP)’:
planar.cpp:369:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
planar.cpp: In function ‘SEXPREC* isKuratowskiSubgraph(SEXP, SEXP, SEXP)’:
planar.cpp:429:36: warning: variable ‘ki_end’ set but not used [-Wunused-but-set-variable]
planar.cpp:461:6: warning: unused variable ‘i’ [-Wunused-variable]
In file included from planar.cpp:5:0:
rbgl_trimmed_boost_1_49_0/boost/graph/planar_canonical_ordering.hpp: In function ‘void boost::planar_canonical_ordering(const Graph&, PlanarEmbedding, OutputIterator, VertexIndexMap) [with Graph = boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_index_t, int>, boost::property<boost::edge_index_t, int> >, PlanarEmbedding = boost::iterator_property_map<__gnu_cxx::__normal_iterator<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> >*, std::vector<std::vector<boost::detail::edge_desc_impl<boost::undirected_tag, long unsigned int> > > >, boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, long unsigned int> >, OutputIterator = std::back_insert_iterator<std::vector<long unsigned int> >, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, int>, long unsigned int>]’:
rbgl_trimmed_boost_1_49_0/boost/graph/planar_canonical_ordering.hpp:149:17: warning: ‘second_vertex’ may be used uninitialized in this function [-Wuninitialized]
In file included from planar.cpp:11:0:
rbgl_trimmed_boost_1_49_0/boost/graph/max_cardinality_matching.hpp: In member function ‘bool boost::edmonds_augmenting_path_finder<Graph, MateMap, VertexIndexMap>::augment_matching() [with Graph = R_adjacency_list<boost::undirectedS, int>, MateMap = long unsigned int*, VertexIndexMap = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>]’:
rbgl_trimmed_boost_1_49_0/boost/graph/max_cardinality_matching.hpp:334:7: warning: ‘w’ may be used uninitialized in this function [-Wuninitialized]
rbgl_trimmed_boost_1_49_0/boost/graph/max_cardinality_matching.hpp:333:7: warning: ‘v’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c shortestPath.cpp -o shortestPath.o
In file included from shortestPath.cpp:4:0:
rbgl_trimmed_boost_1_49_0/boost/graph/johnson_all_pairs_shortest.hpp: In function ‘bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, const BinaryPredicate&, const BinaryFunction&, const Infinity&, DistanceZero) [with VertexAndEdgeListGraph = R_adjacency_list<boost::directedS, double>, DistanceMatrix = Basic2DMatrix<double>, VertexID = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>, Weight = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>, BinaryPredicate = std::less<double>, BinaryFunction = boost::closed_plus<double>, Infinity = double, DistanceZero = double]’:
rbgl_trimmed_boost_1_49_0/boost/graph/johnson_all_pairs_shortest.hpp:171:67:   instantiated from ‘bool boost::detail::johnson_dispatch(VertexAndEdgeListGraph&, DistanceMatrix&, const boost::bgl_named_params<P, T, R>&, Weight, VertexID) [with VertexAndEdgeListGraph = R_adjacency_list<boost::directedS, double>, DistanceMatrix = Basic2DMatrix<double>, P = int, T = int, R = boost::no_property, Weight = boost::adj_list_edge_property_map<boost::directed_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>, VertexID = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>]’
rbgl_trimmed_boost_1_49_0/boost/graph/johnson_all_pairs_shortest.hpp:198:63:   instantiated from ‘bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&) [with VertexAndEdgeListGraph = R_adjacency_list<boost::directedS, double>, DistanceMatrix = Basic2DMatrix<double>]’
shortestPath.cpp:56:46:   instantiated from here
rbgl_trimmed_boost_1_49_0/boost/graph/johnson_all_pairs_shortest.hpp:124:49: warning: variable ‘u1’ set but not used [-Wunused-but-set-variable]
rbgl_trimmed_boost_1_49_0/boost/graph/johnson_all_pairs_shortest.hpp:124:53: warning: variable ‘v1’ set but not used [-Wunused-but-set-variable]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c sna.cpp -o sna.o
sna.cpp: In function ‘SEXPREC* lambdaSets(SEXP, SEXP, SEXP, SEXP)’:
sna.cpp:161:9: warning: variable ‘res_cap’ set but not used [-Wunused-but-set-variable]
In file included from sna.cpp:3:0:
rbgl_trimmed_boost_1_49_0/boost/graph/johnson_all_pairs_shortest.hpp: In function ‘bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&, VertexID, Weight, const BinaryPredicate&, const BinaryFunction&, const Infinity&, DistanceZero) [with VertexAndEdgeListGraph = R_adjacency_list<boost::undirectedS, double>, DistanceMatrix = Basic2DMatrix<double>, VertexID = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>, Weight = boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>, BinaryPredicate = std::less<double>, BinaryFunction = boost::closed_plus<double>, Infinity = double, DistanceZero = double]’:
rbgl_trimmed_boost_1_49_0/boost/graph/johnson_all_pairs_shortest.hpp:171:67:   instantiated from ‘bool boost::detail::johnson_dispatch(VertexAndEdgeListGraph&, DistanceMatrix&, const boost::bgl_named_params<P, T, R>&, Weight, VertexID) [with VertexAndEdgeListGraph = R_adjacency_list<boost::undirectedS, double>, DistanceMatrix = Basic2DMatrix<double>, P = int, T = int, R = boost::no_property, Weight = boost::adj_list_edge_property_map<boost::undirected_tag, double, double&, long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property>, boost::edge_weight_t>, VertexID = boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_color_t, boost::default_color_type>, long unsigned int>]’
rbgl_trimmed_boost_1_49_0/boost/graph/johnson_all_pairs_shortest.hpp:198:63:   instantiated from ‘bool boost::johnson_all_pairs_shortest_paths(VertexAndEdgeListGraph&, DistanceMatrix&) [with VertexAndEdgeListGraph = R_adjacency_list<boost::undirectedS, double>, DistanceMatrix = Basic2DMatrix<double>]’
sna.cpp:105:46:   instantiated from here
rbgl_trimmed_boost_1_49_0/boost/graph/johnson_all_pairs_shortest.hpp:124:49: warning: variable ‘u1’ set but not used [-Wunused-but-set-variable]
rbgl_trimmed_boost_1_49_0/boost/graph/johnson_all_pairs_shortest.hpp:124:53: warning: variable ‘v1’ set but not used [-Wunused-but-set-variable]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c transitive_closure.cpp -o transitive_closure.o
rbgl_trimmed_boost_1_49_0/boost/graph/detail/adj_list_edge_iterator.hpp: In function ‘SEXPREC* BGL_transitive_closure_D(SEXP, SEXP, SEXP)’:
rbgl_trimmed_boost_1_49_0/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: ‘*((void*)(& ei)+48).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::<anonymous>.boost::iterator_adaptor<boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>, __gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, boost::use_default, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_iterator.__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >::_M_current’ may be used uninitialized in this function [-Wuninitialized]
transitive_closure.cpp:43:33: note: ‘*((void*)(& ei)+48).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::<anonymous>.boost::iterator_adaptor<boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>, __gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, boost::use_default, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_iterator.__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >::_M_current’ was declared here
transitive_closure.cpp:46:50: warning: ‘*((void*)(& ei)+32).boost::detail::out_edge_iter<__gnu_cxx::__normal_iterator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >*, std::vector<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> >, std::allocator<boost::detail::sep_<long unsigned int, boost::property<boost::edge_weight_t, double, boost::no_property> > > > >, long unsigned int, boost::detail::edge_desc_impl<boost::directed_tag, long unsigned int>, long int>::m_src’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include   -Irbgl_trimmed_boost_1_49_0 -fpic  -g -O2  -Wall -c wavefront.cpp -o wavefront.o
g++ -shared -L/usr/local/lib -o RBGL.so bbc.o cliques.o clusteringCoef.o dominatorTree.o edmonds_optimum_branching.o hcs.o incrConnComp.o interfaces.o minST.o mincut.o ordering.o planar.o shortestPath.o sna.o transitive_closure.o wavefront.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/RBGL.Rcheck/RBGL/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RBGL)

RBGL.Rcheck/RBGL-Ex.timings:

nameusersystemelapsed
FileDep0.5920.0120.607
astarSearch0.0120.0000.012
bandwidth0.0240.0000.024
bccluster0.0160.0000.018
bellman.ford.sp0.0160.0000.015
betweenness0.0120.0000.016
bfs0.0240.0080.029
biConnComp0.0120.0040.016
chrobakPayneStraightLineDrawing0.0160.0040.023
clusteringCoef0.0720.0040.075
clusteringCoefAppr0.0120.0040.017
coloring0.0120.0000.012
connectedComp0.0240.0040.077
dag.sp0.0120.0040.016
dijkstra.sp0.0360.0000.035
dominatorTree0.0120.0000.013
edgeConn0.0120.0040.013
edmondsMaxCardinalityMatching0.0280.0000.027
edmondsOptimumBranching0.0120.0000.013
extractPath0.0080.0000.007
floyd.warshall.all.pairs.sp0.0120.0000.015
gprofile0.0080.0040.013
graphGenerator0.0040.0000.003
highlyConnSG0.0120.0040.016
incrConnComp0.0120.0040.016
is.triangulated0.0200.0040.023
isKuratowskiSubgraph0.0160.0000.019
isStraightLineDrawing0.0200.0000.024
isomorphism0.0120.0080.023
johnson.all.pairs.sp0.0040.0120.014
kCliques0.0160.0000.015
kCores0.0440.0120.058
lambdaSets0.0160.0000.017
layout0.0040.0000.006
makeBiconnectedPlanar0.0240.0000.024
makeConnected0.0160.0000.016
makeMaximalPlanar0.0160.0000.019
maxClique0.0280.0000.026
maxFlow0.0200.0040.023
minCut0.0160.0000.014
mstree.kruskal0.0360.0000.036
mstree.prim0.0120.0040.018
ordering0.0200.0000.019
planarCanonicalOrdering0.0160.0000.015
planarFaceTraversal0.0160.0040.018
removeSelfLoops0.0120.0080.021
separates0.0200.0000.022
sp.between0.0960.0000.095
strongComp0.0160.0000.019
transClosure0.0160.0000.015
transitivity0.0080.0040.014
tsort0.0080.0040.011
wavefront0.0120.0000.014