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BioC 2.14: CHECK report for RBGL on zin2

This page was generated on 2014-10-08 08:47:35 -0700 (Wed, 08 Oct 2014).

Package 632/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RBGL 1.40.1
Bioconductor Package Maintainer
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/RBGL
Last Changed Rev: 93449 / Revision: 95116
Last Changed Date: 2014-08-18 11:54:42 -0700 (Mon, 18 Aug 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: RBGL
Version: 1.40.1
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings RBGL_1.40.1.tar.gz
StartedAt: 2014-10-08 02:08:45 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 02:10:38 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 113.5 seconds
RetCode: 0
Status:  OK 
CheckDir: RBGL.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings RBGL_1.40.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/RBGL.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.40.1’
* 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/85s] 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 files in ‘vignettes’ ... OK
* checking examples ... [2s/2s] 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 3 notes.
See
  ‘/home/biocbuild/bbs-2.14-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-2.14-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-2.14-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-2.14-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-2.14-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-2.14-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-2.14-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-2.14-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-2.14-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-2.14-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-2.14-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-2.14-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-2.14-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-2.14-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-2.14-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-2.14-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-2.14-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-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-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
FileDep0.5520.0080.565
astarSearch0.0080.0000.007
bandwidth0.0120.0040.018
bccluster0.0120.0000.014
bellman.ford.sp0.0120.0000.012
betweenness0.0040.0040.010
bfs0.0200.0040.025
biConnComp0.0080.0040.009
chrobakPayneStraightLineDrawing0.0120.0000.011
clusteringCoef0.0120.0000.014
clusteringCoefAppr0.0080.0000.011
coloring0.0080.0000.009
connectedComp0.0240.0000.048
dag.sp0.0120.0040.013
dijkstra.sp0.0320.0000.031
dominatorTree0.0080.0000.009
edgeConn0.0080.0000.009
edmondsMaxCardinalityMatching0.0680.0040.070
edmondsOptimumBranching0.0080.0000.008
extractPath0.0040.0000.003
floyd.warshall.all.pairs.sp0.0120.0000.010
gprofile0.0080.0000.007
graphGenerator0.0040.0000.001
highlyConnSG0.0120.0000.013
incrConnComp0.0120.0000.009
is.triangulated0.0160.0000.016
isKuratowskiSubgraph0.0080.0040.012
isStraightLineDrawing0.0120.0000.013
isomorphism0.0120.0000.014
johnson.all.pairs.sp0.0080.0000.009
kCliques0.0080.0040.009
kCores0.0440.0000.044
lambdaSets0.0120.0000.011
layout0.0000.0000.001
makeBiconnectedPlanar0.0160.0000.014
makeConnected0.0120.0000.010
makeMaximalPlanar0.0120.0000.011
maxClique0.0160.0040.018
maxFlow0.0160.0000.015
minCut0.0080.0000.009
mstree.kruskal0.0280.0000.027
mstree.prim0.0120.0000.009
ordering0.0120.0000.014
planarCanonicalOrdering0.0080.0000.009
planarFaceTraversal0.0120.0000.011
removeSelfLoops0.0120.0000.013
separates0.0160.0000.016
sp.between0.0280.0000.030
strongComp0.0160.0000.016
transClosure0.0120.0000.011
transitivity0.0040.0040.010
tsort0.0040.0000.005
wavefront0.0040.0040.009