NetPathMiner

Package: NetPathMiner
Version: 1.8.0
Date: 2014 onwards
Title: NetPathMiner for Biological Network Construction, Path Mining
and Visualization
Author: Ahmed Mohamed <mohamed@kuicr.kyoto-u.ac.jp>, Tim Hancock
<timothy.hancock@kuicr.kyoto-u.ac.jp>, Ichigaku Takigawa
<takigawa@kuicr.kyoto-u.ac.jp>, Nicolas Wicker
<nicolas.wicker@unistra.fr>
Maintainer: Ahmed Mohamed <mohamed@kuicr.kyoto-u.ac.jp>
Description: NetPathMiner is a general framework for network path
mining using genome-scale networks. It constructs networks from
KGML, SBML and BioPAX files, providing three network
representations, metabolic, reaction and gene representations.
NetPathMiner finds active paths and applies machine learning
methods to summarize found paths for easy interpretation. It
also provides static and interactive visualizations of networks
and paths to aid manual investigation.
Depends: R (>= 3.0.2), igraph (>= 1.0)
Suggests: rBiopaxParser (>= 2.1), RCurl, RCytoscape, graph
License: GPL (>= 2)
URL: https://github.com/ahmohamed/NetPathMiner
NeedsCompilation: yes
SystemRequirements: libxml2, libSBML (>= 5.5)
Biarch: TRUE
biocViews: GraphAndNetwork, Pathways, Network, Clustering,
Classification
Packaged: 2016-05-04 05:28:16 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'NetPathMiner' ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for xmlParseFile in -lxml2... yes
checking for readSBML in -lsbml... no
untarring boost include tree...
SBML not found.
libXML2 found
checking for xml2-config... /usr/bin/xml2-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I . -I/usr/local/include -fpic  -g -O2  -c PathRanker.cpp -o PathRanker.o
In file included from ./boost/type_traits.hpp:22:0,
                 from ./boost/pending/property.hpp:13,
                 from ./boost/graph/graph_traits.hpp:27,
                 from ./boost/graph/graph_utility.hpp:29,
                 from PathRanker.cpp:17:
./boost/type_traits/common_type.hpp:69:22: warning: variadic templates only available with -std=c++11 or -std=gnu++11
     template<typename... T>
                      ^
./boost/type_traits/common_type.hpp:149:46: warning: variadic templates only available with -std=c++11 or -std=gnu++11
     template<typename T, typename U, typename... V>
                                              ^
In file included from ./boost/unordered/detail/buckets.hpp:15:0,
                 from ./boost/unordered/detail/table.hpp:10,
                 from ./boost/unordered/detail/equivalent.hpp:14,
                 from ./boost/unordered/unordered_set.hpp:17,
                 from ./boost/unordered_set.hpp:16,
                 from ./boost/pending/container_traits.hpp:22,
                 from ./boost/graph/graph_utility.hpp:31,
                 from PathRanker.cpp:17:
./boost/unordered/detail/allocate.hpp:437:55: warning: variadic templates only available with -std=c++11 or -std=gnu++11
     template <typename T, typename ValueType, typename... Args>
                                                       ^
./boost/unordered/detail/allocate.hpp:561:39: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <typename T, typename... Args>
                                       ^
./boost/unordered/detail/allocate.hpp:565:62: warning: variadic templates only available with -std=c++11 or -std=gnu++11
             construct(Alloc& a, T* p, BOOST_FWD_REF(Args)... x)
                                                              ^
./boost/unordered/detail/allocate.hpp:570:39: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <typename T, typename... Args>
                                       ^
./boost/unordered/detail/allocate.hpp:574:60: warning: variadic templates only available with -std=c++11 or -std=gnu++11
             construct(Alloc&, T* p, BOOST_FWD_REF(Args)... x)
                                                            ^
./boost/unordered/detail/allocate.hpp:770:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
     template <typename Alloc, typename T, typename... Args>
                                                   ^
./boost/unordered/detail/allocate.hpp:772:32: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         BOOST_FWD_REF(Args)... args)
                                ^
./boost/unordered/detail/allocate.hpp:944:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
     template <typename Alloc, typename T, typename... Args>
                                                   ^
./boost/unordered/detail/allocate.hpp:946:32: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         BOOST_FWD_REF(Args)... args)
                                ^
In file included from ./boost/unordered/detail/buckets.hpp:15:0,
                 from ./boost/unordered/detail/table.hpp:10,
                 from ./boost/unordered/detail/equivalent.hpp:14,
                 from ./boost/unordered/unordered_set.hpp:17,
                 from ./boost/unordered_set.hpp:16,
                 from ./boost/pending/container_traits.hpp:22,
                 from ./boost/graph/graph_utility.hpp:31,
                 from PathRanker.cpp:17:
./boost/unordered/detail/allocate.hpp:90:50: warning: variadic templates only available with -std=c++11 or -std=gnu++11
 #define BOOST_UNORDERED_EMPLACE_TEMPLATE typename... Args
                                                  ^
./boost/unordered/detail/buckets.hpp:344:19: note: in expansion of macro 'BOOST_UNORDERED_EMPLACE_TEMPLATE'
         template <BOOST_UNORDERED_EMPLACE_TEMPLATE>
                   ^
./boost/unordered/detail/allocate.hpp:91:61: warning: variadic templates only available with -std=c++11 or -std=gnu++11
 #define BOOST_UNORDERED_EMPLACE_ARGS BOOST_FWD_REF(Args)... args
                                                             ^
./boost/unordered/detail/buckets.hpp:345:35: note: in expansion of macro 'BOOST_UNORDERED_EMPLACE_ARGS'
         void construct_with_value(BOOST_UNORDERED_EMPLACE_ARGS)
                                   ^
In file included from ./boost/unordered/detail/equivalent.hpp:15:0,
                 from ./boost/unordered/unordered_set.hpp:17,
                 from ./boost/unordered_set.hpp:16,
                 from ./boost/pending/container_traits.hpp:22,
                 from ./boost/graph/graph_utility.hpp:31,
                 from PathRanker.cpp:17:
./boost/unordered/detail/extract_key.hpp:60:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <class... Args>
                        ^
./boost/unordered/detail/extract_key.hpp:61:42: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         static no_key extract(Args const&...)
                                          ^
./boost/unordered/detail/extract_key.hpp:111:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <class... Args>
                        ^
./boost/unordered/detail/extract_key.hpp:112:42: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         static no_key extract(Args const&...)
                                          ^
In file included from ./boost/unordered/detail/buckets.hpp:15:0,
                 from ./boost/unordered/detail/table.hpp:10,
                 from ./boost/unordered/detail/equivalent.hpp:14,
                 from ./boost/unordered/unordered_set.hpp:17,
                 from ./boost/unordered_set.hpp:16,
                 from ./boost/pending/container_traits.hpp:22,
                 from ./boost/graph/graph_utility.hpp:31,
                 from PathRanker.cpp:17:
./boost/unordered/detail/allocate.hpp:90:50: warning: variadic templates only available with -std=c++11 or -std=gnu++11
 #define BOOST_UNORDERED_EMPLACE_TEMPLATE typename... Args
                                                  ^
./boost/unordered/detail/equivalent.hpp:459:19: note: in expansion of macro 'BOOST_UNORDERED_EMPLACE_TEMPLATE'
         template <BOOST_UNORDERED_EMPLACE_TEMPLATE>
                   ^
./boost/unordered/detail/allocate.hpp:91:61: warning: variadic templates only available with -std=c++11 or -std=gnu++11
 #define BOOST_UNORDERED_EMPLACE_ARGS BOOST_FWD_REF(Args)... args
                                                             ^
./boost/unordered/detail/equivalent.hpp:460:26: note: in expansion of macro 'BOOST_UNORDERED_EMPLACE_ARGS'
         iterator emplace(BOOST_UNORDERED_EMPLACE_ARGS)
                          ^
./boost/unordered/detail/allocate.hpp:90:50: warning: variadic templates only available with -std=c++11 or -std=gnu++11
 #define BOOST_UNORDERED_EMPLACE_TEMPLATE typename... Args
                                                  ^
./boost/unordered/detail/unique.hpp:374:19: note: in expansion of macro 'BOOST_UNORDERED_EMPLACE_TEMPLATE'
         template <BOOST_UNORDERED_EMPLACE_TEMPLATE>
                   ^
./boost/unordered/detail/allocate.hpp:91:61: warning: variadic templates only available with -std=c++11 or -std=gnu++11
 #define BOOST_UNORDERED_EMPLACE_ARGS BOOST_FWD_REF(Args)... args
                                                             ^
./boost/unordered/detail/unique.hpp:375:32: note: in expansion of macro 'BOOST_UNORDERED_EMPLACE_ARGS'
         emplace_return emplace(BOOST_UNORDERED_EMPLACE_ARGS)
                                ^
./boost/unordered/detail/allocate.hpp:90:50: warning: variadic templates only available with -std=c++11 or -std=gnu++11
 #define BOOST_UNORDERED_EMPLACE_TEMPLATE typename... Args
                                                  ^
./boost/unordered/detail/unique.hpp:397:19: note: in expansion of macro 'BOOST_UNORDERED_EMPLACE_TEMPLATE'
         template <BOOST_UNORDERED_EMPLACE_TEMPLATE>
                   ^
./boost/unordered/detail/allocate.hpp:91:61: warning: variadic templates only available with -std=c++11 or -std=gnu++11
 #define BOOST_UNORDERED_EMPLACE_ARGS BOOST_FWD_REF(Args)... args
                                                             ^
./boost/unordered/detail/unique.hpp:399:13: note: in expansion of macro 'BOOST_UNORDERED_EMPLACE_ARGS'
             BOOST_UNORDERED_EMPLACE_ARGS)
             ^
./boost/unordered/detail/allocate.hpp:90:50: warning: variadic templates only available with -std=c++11 or -std=gnu++11
 #define BOOST_UNORDERED_EMPLACE_TEMPLATE typename... Args
                                                  ^
./boost/unordered/detail/unique.hpp:431:19: note: in expansion of macro 'BOOST_UNORDERED_EMPLACE_TEMPLATE'
         template <BOOST_UNORDERED_EMPLACE_TEMPLATE>
                   ^
./boost/unordered/detail/allocate.hpp:91:61: warning: variadic templates only available with -std=c++11 or -std=gnu++11
 #define BOOST_UNORDERED_EMPLACE_ARGS BOOST_FWD_REF(Args)... args
                                                             ^
./boost/unordered/detail/unique.hpp:432:45: note: in expansion of macro 'BOOST_UNORDERED_EMPLACE_ARGS'
         emplace_return emplace_impl(no_key, BOOST_UNORDERED_EMPLACE_ARGS)
                                             ^
In file included from ./boost/unordered_set.hpp:16:0,
                 from ./boost/pending/container_traits.hpp:22,
                 from ./boost/graph/graph_utility.hpp:31,
                 from PathRanker.cpp:17:
./boost/unordered/unordered_set.hpp:233:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <class... Args>
                        ^
./boost/unordered/unordered_set.hpp:234:66: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         std::pair<iterator, bool> emplace(BOOST_FWD_REF(Args)... args)
                                                                  ^
./boost/unordered/unordered_set.hpp:239:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <class... Args>
                        ^
./boost/unordered/unordered_set.hpp:240:70: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         iterator emplace_hint(const_iterator, BOOST_FWD_REF(Args)... args)
                                                                      ^
./boost/unordered/unordered_set.hpp:701:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <class... Args>
                        ^
./boost/unordered/unordered_set.hpp:702:49: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         iterator emplace(BOOST_FWD_REF(Args)... args)
                                                 ^
./boost/unordered/unordered_set.hpp:707:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <class... Args>
                        ^
./boost/unordered/unordered_set.hpp:708:70: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         iterator emplace_hint(const_iterator, BOOST_FWD_REF(Args)... args)
                                                                      ^
In file included from ./boost/unordered_map.hpp:16:0,
                 from ./boost/pending/container_traits.hpp:23,
                 from ./boost/graph/graph_utility.hpp:31,
                 from PathRanker.cpp:17:
./boost/unordered/unordered_map.hpp:235:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <class... Args>
                        ^
./boost/unordered/unordered_map.hpp:236:66: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         std::pair<iterator, bool> emplace(BOOST_FWD_REF(Args)... args)
                                                                  ^
./boost/unordered/unordered_map.hpp:241:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <class... Args>
                        ^
./boost/unordered/unordered_map.hpp:242:70: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         iterator emplace_hint(const_iterator, BOOST_FWD_REF(Args)... args)
                                                                      ^
./boost/unordered/unordered_map.hpp:717:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <class... Args>
                        ^
./boost/unordered/unordered_map.hpp:718:49: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         iterator emplace(BOOST_FWD_REF(Args)... args)
                                                 ^
./boost/unordered/unordered_map.hpp:723:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <class... Args>
                        ^
./boost/unordered/unordered_map.hpp:724:70: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         iterator emplace_hint(const_iterator, BOOST_FWD_REF(Args)... args)
                                                                      ^
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c handlesegfault.c -o handlesegfault.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c hme3m.c -o hme3m.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I . -I/usr/local/include -fpic  -g -O2  -c kgml_interface.cpp -o kgml_interface.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I . -I/usr/local/include -fpic  -g -O2  -c methods.cpp -o methods.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I . -I/usr/local/include -fpic  -g -O2  -c pathScope.cpp -o pathScope.o
In file included from ./boost/type_traits.hpp:22:0,
                 from ./boost/pending/property.hpp:13,
                 from ./boost/graph/graph_traits.hpp:27,
                 from ./boost/graph/graph_utility.hpp:29,
                 from pathScope.cpp:22:
./boost/type_traits/common_type.hpp:69:22: warning: variadic templates only available with -std=c++11 or -std=gnu++11
     template<typename... T>
                      ^
./boost/type_traits/common_type.hpp:149:46: warning: variadic templates only available with -std=c++11 or -std=gnu++11
     template<typename T, typename U, typename... V>
                                              ^
In file included from ./boost/unordered/detail/buckets.hpp:15:0,
                 from ./boost/unordered/detail/table.hpp:10,
                 from ./boost/unordered/detail/equivalent.hpp:14,
                 from ./boost/unordered/unordered_set.hpp:17,
                 from ./boost/unordered_set.hpp:16,
                 from ./boost/pending/container_traits.hpp:22,
                 from ./boost/graph/graph_utility.hpp:31,
                 from pathScope.cpp:22:
./boost/unordered/detail/allocate.hpp:437:55: warning: variadic templates only available with -std=c++11 or -std=gnu++11
     template <typename T, typename ValueType, typename... Args>
                                                       ^
./boost/unordered/detail/allocate.hpp:561:39: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <typename T, typename... Args>
                                       ^
./boost/unordered/detail/allocate.hpp:565:62: warning: variadic templates only available with -std=c++11 or -std=gnu++11
             construct(Alloc& a, T* p, BOOST_FWD_REF(Args)... x)
                                                              ^
./boost/unordered/detail/allocate.hpp:570:39: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <typename T, typename... Args>
                                       ^
./boost/unordered/detail/allocate.hpp:574:60: warning: variadic templates only available with -std=c++11 or -std=gnu++11
             construct(Alloc&, T* p, BOOST_FWD_REF(Args)... x)
                                                            ^
./boost/unordered/detail/allocate.hpp:770:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
     template <typename Alloc, typename T, typename... Args>
                                                   ^
./boost/unordered/detail/allocate.hpp:772:32: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         BOOST_FWD_REF(Args)... args)
                                ^
./boost/unordered/detail/allocate.hpp:944:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
     template <typename Alloc, typename T, typename... Args>
                                                   ^
./boost/unordered/detail/allocate.hpp:946:32: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         BOOST_FWD_REF(Args)... args)
                                ^
In file included from ./boost/unordered/detail/buckets.hpp:15:0,
                 from ./boost/unordered/detail/table.hpp:10,
                 from ./boost/unordered/detail/equivalent.hpp:14,
                 from ./boost/unordered/unordered_set.hpp:17,
                 from ./boost/unordered_set.hpp:16,
                 from ./boost/pending/container_traits.hpp:22,
                 from ./boost/graph/graph_utility.hpp:31,
                 from pathScope.cpp:22:
./boost/unordered/detail/allocate.hpp:90:50: warning: variadic templates only available with -std=c++11 or -std=gnu++11
 #define BOOST_UNORDERED_EMPLACE_TEMPLATE typename... Args
                                                  ^
./boost/unordered/detail/buckets.hpp:344:19: note: in expansion of macro 'BOOST_UNORDERED_EMPLACE_TEMPLATE'
         template <BOOST_UNORDERED_EMPLACE_TEMPLATE>
                   ^
./boost/unordered/detail/allocate.hpp:91:61: warning: variadic templates only available with -std=c++11 or -std=gnu++11
 #define BOOST_UNORDERED_EMPLACE_ARGS BOOST_FWD_REF(Args)... args
                                                             ^
./boost/unordered/detail/buckets.hpp:345:35: note: in expansion of macro 'BOOST_UNORDERED_EMPLACE_ARGS'
         void construct_with_value(BOOST_UNORDERED_EMPLACE_ARGS)
                                   ^
In file included from ./boost/unordered/detail/equivalent.hpp:15:0,
                 from ./boost/unordered/unordered_set.hpp:17,
                 from ./boost/unordered_set.hpp:16,
                 from ./boost/pending/container_traits.hpp:22,
                 from ./boost/graph/graph_utility.hpp:31,
                 from pathScope.cpp:22:
./boost/unordered/detail/extract_key.hpp:60:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <class... Args>
                        ^
./boost/unordered/detail/extract_key.hpp:61:42: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         static no_key extract(Args const&...)
                                          ^
./boost/unordered/detail/extract_key.hpp:111:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <class... Args>
                        ^
./boost/unordered/detail/extract_key.hpp:112:42: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         static no_key extract(Args const&...)
                                          ^
In file included from ./boost/unordered/detail/buckets.hpp:15:0,
                 from ./boost/unordered/detail/table.hpp:10,
                 from ./boost/unordered/detail/equivalent.hpp:14,
                 from ./boost/unordered/unordered_set.hpp:17,
                 from ./boost/unordered_set.hpp:16,
                 from ./boost/pending/container_traits.hpp:22,
                 from ./boost/graph/graph_utility.hpp:31,
                 from pathScope.cpp:22:
./boost/unordered/detail/allocate.hpp:90:50: warning: variadic templates only available with -std=c++11 or -std=gnu++11
 #define BOOST_UNORDERED_EMPLACE_TEMPLATE typename... Args
                                                  ^
./boost/unordered/detail/equivalent.hpp:459:19: note: in expansion of macro 'BOOST_UNORDERED_EMPLACE_TEMPLATE'
         template <BOOST_UNORDERED_EMPLACE_TEMPLATE>
                   ^
./boost/unordered/detail/allocate.hpp:91:61: warning: variadic templates only available with -std=c++11 or -std=gnu++11
 #define BOOST_UNORDERED_EMPLACE_ARGS BOOST_FWD_REF(Args)... args
                                                             ^
./boost/unordered/detail/equivalent.hpp:460:26: note: in expansion of macro 'BOOST_UNORDERED_EMPLACE_ARGS'
         iterator emplace(BOOST_UNORDERED_EMPLACE_ARGS)
                          ^
./boost/unordered/detail/allocate.hpp:90:50: warning: variadic templates only available with -std=c++11 or -std=gnu++11
 #define BOOST_UNORDERED_EMPLACE_TEMPLATE typename... Args
                                                  ^
./boost/unordered/detail/unique.hpp:374:19: note: in expansion of macro 'BOOST_UNORDERED_EMPLACE_TEMPLATE'
         template <BOOST_UNORDERED_EMPLACE_TEMPLATE>
                   ^
./boost/unordered/detail/allocate.hpp:91:61: warning: variadic templates only available with -std=c++11 or -std=gnu++11
 #define BOOST_UNORDERED_EMPLACE_ARGS BOOST_FWD_REF(Args)... args
                                                             ^
./boost/unordered/detail/unique.hpp:375:32: note: in expansion of macro 'BOOST_UNORDERED_EMPLACE_ARGS'
         emplace_return emplace(BOOST_UNORDERED_EMPLACE_ARGS)
                                ^
./boost/unordered/detail/allocate.hpp:90:50: warning: variadic templates only available with -std=c++11 or -std=gnu++11
 #define BOOST_UNORDERED_EMPLACE_TEMPLATE typename... Args
                                                  ^
./boost/unordered/detail/unique.hpp:397:19: note: in expansion of macro 'BOOST_UNORDERED_EMPLACE_TEMPLATE'
         template <BOOST_UNORDERED_EMPLACE_TEMPLATE>
                   ^
./boost/unordered/detail/allocate.hpp:91:61: warning: variadic templates only available with -std=c++11 or -std=gnu++11
 #define BOOST_UNORDERED_EMPLACE_ARGS BOOST_FWD_REF(Args)... args
                                                             ^
./boost/unordered/detail/unique.hpp:399:13: note: in expansion of macro 'BOOST_UNORDERED_EMPLACE_ARGS'
             BOOST_UNORDERED_EMPLACE_ARGS)
             ^
./boost/unordered/detail/allocate.hpp:90:50: warning: variadic templates only available with -std=c++11 or -std=gnu++11
 #define BOOST_UNORDERED_EMPLACE_TEMPLATE typename... Args
                                                  ^
./boost/unordered/detail/unique.hpp:431:19: note: in expansion of macro 'BOOST_UNORDERED_EMPLACE_TEMPLATE'
         template <BOOST_UNORDERED_EMPLACE_TEMPLATE>
                   ^
./boost/unordered/detail/allocate.hpp:91:61: warning: variadic templates only available with -std=c++11 or -std=gnu++11
 #define BOOST_UNORDERED_EMPLACE_ARGS BOOST_FWD_REF(Args)... args
                                                             ^
./boost/unordered/detail/unique.hpp:432:45: note: in expansion of macro 'BOOST_UNORDERED_EMPLACE_ARGS'
         emplace_return emplace_impl(no_key, BOOST_UNORDERED_EMPLACE_ARGS)
                                             ^
In file included from ./boost/unordered_set.hpp:16:0,
                 from ./boost/pending/container_traits.hpp:22,
                 from ./boost/graph/graph_utility.hpp:31,
                 from pathScope.cpp:22:
./boost/unordered/unordered_set.hpp:233:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <class... Args>
                        ^
./boost/unordered/unordered_set.hpp:234:66: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         std::pair<iterator, bool> emplace(BOOST_FWD_REF(Args)... args)
                                                                  ^
./boost/unordered/unordered_set.hpp:239:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <class... Args>
                        ^
./boost/unordered/unordered_set.hpp:240:70: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         iterator emplace_hint(const_iterator, BOOST_FWD_REF(Args)... args)
                                                                      ^
./boost/unordered/unordered_set.hpp:701:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <class... Args>
                        ^
./boost/unordered/unordered_set.hpp:702:49: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         iterator emplace(BOOST_FWD_REF(Args)... args)
                                                 ^
./boost/unordered/unordered_set.hpp:707:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <class... Args>
                        ^
./boost/unordered/unordered_set.hpp:708:70: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         iterator emplace_hint(const_iterator, BOOST_FWD_REF(Args)... args)
                                                                      ^
In file included from ./boost/unordered_map.hpp:16:0,
                 from ./boost/pending/container_traits.hpp:23,
                 from ./boost/graph/graph_utility.hpp:31,
                 from pathScope.cpp:22:
./boost/unordered/unordered_map.hpp:235:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <class... Args>
                        ^
./boost/unordered/unordered_map.hpp:236:66: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         std::pair<iterator, bool> emplace(BOOST_FWD_REF(Args)... args)
                                                                  ^
./boost/unordered/unordered_map.hpp:241:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <class... Args>
                        ^
./boost/unordered/unordered_map.hpp:242:70: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         iterator emplace_hint(const_iterator, BOOST_FWD_REF(Args)... args)
                                                                      ^
./boost/unordered/unordered_map.hpp:717:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <class... Args>
                        ^
./boost/unordered/unordered_map.hpp:718:49: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         iterator emplace(BOOST_FWD_REF(Args)... args)
                                                 ^
./boost/unordered/unordered_map.hpp:723:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         template <class... Args>
                        ^
./boost/unordered/unordered_map.hpp:724:70: warning: variadic templates only available with -std=c++11 or -std=gnu++11
         iterator emplace_hint(const_iterator, BOOST_FWD_REF(Args)... args)
                                                                      ^
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o NetPathMiner.so PathRanker.o handlesegfault.o hme3m.o init.o kgml_interface.o methods.o pathScope.o -lxml2 -L/home/ddbj/local/lib64/R/lib -lRlapack -L/home/ddbj/local/lib64/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/NetPathMiner/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'NetPathMiner'
    finding HTML links ... done
    KGML2igraph                             html  
    MIRIAM                                  html  
    NPMdefaults                             html  
    NetPathMiner-package                    html  
    SBML2igraph                             html  
    assignEdgeWeights                       html  
Rd warning: /tmp/RtmpGmnzN4/R.INSTALL8ac50c2fd6/NetPathMiner/man/assignEdgeWeights.Rd:27: missing file link 'max'
    biopax2igraph                           html  
    colorVertexByAttr                       html  
    ex_biopax                               html  
    ex_kgml_sig                             html  
    ex_microarray                           html  
    ex_sbml                                 html  
    extractPathNetwork                      html  
    getAttr                                 html  
Rd warning: /tmp/RtmpGmnzN4/R.INSTALL8ac50c2fd6/NetPathMiner/man/getAttr.Rd:47: missing file link 'attributes'
    getGeneSetNetworks                      html  
    getGeneSets                             html  
    getPathsAsEIDs                          html  
    layoutVertexByAttr                      html  
Rd warning: /tmp/RtmpGmnzN4/R.INSTALL8ac50c2fd6/NetPathMiner/man/layoutVertexByAttr.Rd:18: missing file link 'layout.fruchterman.reingold'
Rd warning: /tmp/RtmpGmnzN4/R.INSTALL8ac50c2fd6/NetPathMiner/man/layoutVertexByAttr.Rd:18: missing file link 'layout.kamada.kawai'
    makeGeneNetwork                         html  
    makeReactionNetwork                     html  
    pathClassifier                          html  
    pathCluster                             html  
    pathRanker                              html  
    pathsToBinary                           html  
    plotAllNetworks                         html  
    plotClassifierROC                       html  
    plotClusters                            html  
    plotCytoscape                           html  
    plotNetwork                             html  
    plotPathClassifier                      html  
    plotPathCluster                         html  
    plotPaths                               html  
    predictPathClassifier                   html  
    predictPathCluster                      html  
    registerMemoryErr                       html  
    rmSmallCompounds                        html  
    samplePaths                             html  
    simplifyReactionNetwork                 html  
    toGraphNEL                              html  
    vertexDeleteReconnect                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (NetPathMiner)
Making 'packages.html' ... done