[graph-tool] Comiling error of graph tool

Noriyuki Kojima kojimano at umich.edu
Sat Feb 24 00:19:17 CET 2018


Hello, I am encountering the compiling issue of graph-tool 2.26 (latest
version.), when I run command "make -j 16"

I am using,
gcc 5.4.0
boost: 1.66
python: 3.5 (anaconda distribution)
os: CentOS7

Output of "make -j 16" is attached as out.txt.

Output of Configure, using commands "./configure
CXX="/sw/arcts/centos7/gcc/5.4.0/bin/g++"
LDFLAGS="-L/scratch/jiadeng_fluxoe/kojimano/packages/one_six/lib"
CPPFLAGS="-I/scratch/jiadeng_fluxoe/kojimano/packages/one_six/lib"
--with-python-module-path="/home/kojimano/anaconda3/envs/CogMap2/lib/python3.5/site-packages"
--prefix="/home/kojimano/anaconda3/envs/CogMap2/lib"
--with-boost="/scratch/jiadeng_fluxoe/kojimano/packages/one_six"
-with-boost=yes --disable-cairo --disable-sparsehash
" is attched as out_config.txt, config.log.


-- 
Noriyuki, Kojima
University of Michigan, Engineering
Computer Science
kojimano at umich.edu
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make  all-recursive
make[1]: Entering directory `/scratch/jiadeng_fluxoe/kojimano/CogMap2/gym/MINOS_Cog_Map_Original/deps/graph-tool-2.26'
Making all in src
make[2]: Entering directory `/scratch/jiadeng_fluxoe/kojimano/CogMap2/gym/MINOS_Cog_Map_Original/deps/graph-tool-2.26/src'
Making all in graph
make[3]: Entering directory `/scratch/jiadeng_fluxoe/kojimano/CogMap2/gym/MINOS_Cog_Map_Original/deps/graph-tool-2.26/src/graph'
Making all in centrality
make[4]: Entering directory `/scratch/jiadeng_fluxoe/kojimano/CogMap2/gym/MINOS_Cog_Map_Original/deps/graph-tool-2.26/src/graph/centrality'
  CXX      graph_katz.lo
  CXX      graph_pagerank.lo
  CXXLD    libgraph_tool_centrality.la
make[4]: Leaving directory `/scratch/jiadeng_fluxoe/kojimano/CogMap2/gym/MINOS_Cog_Map_Original/deps/graph-tool-2.26/src/graph/centrality'
Making all in clustering
make[4]: Entering directory `/scratch/jiadeng_fluxoe/kojimano/CogMap2/gym/MINOS_Cog_Map_Original/deps/graph-tool-2.26/src/graph/clustering'
  CXX      graph_clustering.lo
  CXX      graph_extended_clustering.lo
  CXX      graph_motifs.lo
In file included from graph_motifs.cc:26:0:
../../../src/graph/graph_python_interface.hh:85:33: error: 'asymmetric_coroutine' in namespace 'graph_tool::coroutines' does not name a template type
 typedef graph_tool::coroutines::asymmetric_coroutine<boost::python::object>
                                 ^
../../../src/graph/graph_python_interface.hh:107:21: error: 'coro_t' was not declared in this scope
     std::shared_ptr<coro_t::pull_type> _coro;
                     ^
../../../src/graph/graph_python_interface.hh:107:38: error: template argument 1 is invalid
     std::shared_ptr<coro_t::pull_type> _coro;
                                      ^
../../../src/graph/graph_python_interface.hh:108:5: error: 'coro_t' does not name a type
     coro_t::pull_type::iterator _iter;
     ^
../../../src/graph/graph_python_interface.hh:109:5: error: 'coro_t' does not name a type
     coro_t::pull_type::iterator _end;
     ^
../../../src/graph/graph_python_interface.hh: In constructor 'graph_tool::CoroGenerator::CoroGenerator(Dispatch&)':
../../../src/graph/graph_python_interface.hh:93:27: error: 'coro_t' was not declared in this scope
         : _coro(make_coro<coro_t::pull_type>(dispatch)),
                           ^
../../../src/graph/graph_python_interface.hh:93:17: error: parse error in template argument list
         : _coro(make_coro<coro_t::pull_type>(dispatch)),
                 ^
../../../src/graph/graph_python_interface.hh:94:11: error: class 'graph_tool::CoroGenerator' does not have any field named '_iter'
           _iter(begin(*_coro)), _end(end(*_coro)), _first(true) {}
           ^
../../../src/graph/graph_python_interface.hh:94:24: error: invalid type argument of unary '*' (have 'int')
           _iter(begin(*_coro)), _end(end(*_coro)), _first(true) {}
                        ^
../../../src/graph/graph_python_interface.hh:94:29: error: there are no arguments to 'begin' that depend on a template parameter, so a declaration of 'begin' must be available [-fpermissive]
           _iter(begin(*_coro)), _end(end(*_coro)), _first(true) {}
                             ^
../../../src/graph/graph_python_interface.hh:94:29: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated)
../../../src/graph/graph_python_interface.hh:94:33: error: class 'graph_tool::CoroGenerator' does not have any field named '_end'
           _iter(begin(*_coro)), _end(end(*_coro)), _first(true) {}
                                 ^
../../../src/graph/graph_python_interface.hh:94:43: error: invalid type argument of unary '*' (have 'int')
           _iter(begin(*_coro)), _end(end(*_coro)), _first(true) {}
                                           ^
../../../src/graph/graph_python_interface.hh:94:48: error: there are no arguments to 'end' that depend on a template parameter, so a declaration of 'end' must be available [-fpermissive]
           _iter(begin(*_coro)), _end(end(*_coro)), _first(true) {}
                                                ^
../../../src/graph/graph_python_interface.hh: In member function 'boost::python::api::object graph_tool::CoroGenerator::next()':
../../../src/graph/graph_python_interface.hh:100:15: error: '_iter' was not declared in this scope
             ++_iter;
               ^
../../../src/graph/graph_python_interface.hh:101:13: error: '_iter' was not declared in this scope
         if (_iter == _end)
             ^
../../../src/graph/graph_python_interface.hh:101:22: error: '_end' was not declared in this scope
         if (_iter == _end)
                      ^
../../../src/graph/graph_python_interface.hh:103:37: error: '_iter' was not declared in this scope
         boost::python::object oe = *_iter;
                                     ^
make[4]: *** [graph_motifs.lo] Error 1
make[4]: *** Waiting for unfinished jobs....
make[4]: Leaving directory `/scratch/jiadeng_fluxoe/kojimano/CogMap2/gym/MINOS_Cog_Map_Original/deps/graph-tool-2.26/src/graph/clustering'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/scratch/jiadeng_fluxoe/kojimano/CogMap2/gym/MINOS_Cog_Map_Original/deps/graph-tool-2.26/src/graph'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/scratch/jiadeng_fluxoe/kojimano/CogMap2/gym/MINOS_Cog_Map_Original/deps/graph-tool-2.26/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/scratch/jiadeng_fluxoe/kojimano/CogMap2/gym/MINOS_Cog_Map_Original/deps/graph-tool-2.26'
make: *** [all] Error 2
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checking for gcc... gcc
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checking the maximum length of command line arguments... 3458764513820540925
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checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
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checking for Expat XML Parser... yes
checking for a Python interpreter with version >= 2.7... python
checking for python... /home/kojimano/anaconda3/envs/CogMap2/bin/python
checking for python version... 3.5
checking for python platform... linux
checking for python script directory... ${prefix}/lib/python3.5/site-packages
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checking for the distutils Python package... yes
checking for Python include path... -I/home/kojimano/anaconda3/envs/CogMap2/include/python3.5m
checking for Python library path... -L/home/kojimano/anaconda3/envs/CogMap2/lib -lpython3.5m
checking for Python site-packages path... /home/kojimano/anaconda3/envs/CogMap2/lib/python3.5/site-packages
checking python extra libraries... -lpthread -ldl -lutil -lrt -lm
checking python extra linking flags... -Xlinker -export-dynamic
checking consistency of all components of python development environment... yes
checking for boostlib >= 1.55.0 (105500)... configure: We could not detect the boost libraries (version [1.55.0] or higher). If you have a staged boost library (still not installed) please specify $BOOST_ROOT in your environment and do not give a PATH to --with-boost option.  If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation.
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configure: WARNING: No usable boost::coroutine found! Some functionality will be disabled in the library.
checking whether the Boost::Graph library is available... yes
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checking python module: numpy... yes
checking for numpy/arrayobject.h... yes
checking whether to enable sparsehash... no
configure: pkgconfig directory is ${libdir}/pkgconfig
checking our pkgconfig libname... graph-tool-py3.5
checking our pkgconfig version... 2.26
checking our pkgconfig_libdir... ${libdir}/pkgconfig
expanded our pkgconfig_libdir... /home/kojimano/anaconda3/envs/CogMap2/lib/lib/pkgconfig
checking our pkgconfig_libfile... graph-tool-py3.5.pc
checking our package / suffix... graph-tool / 
checking our pkgconfig description... graph-tool Python library
checking our pkgconfig requires... 
checking our pkgconfig ext libs... -L/home/kojimano/anaconda3/envs/CogMap2/lib -lpython3.5m -lboost_python3
checking our pkgconfig cppflags... -I/home/kojimano/anaconda3/envs/CogMap2/lib/python3.5/site-packages/graph_tool/include -I/home/kojimano/anaconda3/envs/CogMap2/lib/python3.5/site-packages/graph_tool/include/boost-workaround -I/home/kojimano/anaconda3/envs/CogMap2/include/python3.5m -pthread -I/include/boost-0 -I/home/kojimano/anaconda3/envs/CogMap2/lib/python3.5/site-packages/numpy/core/include
checking our pkgconfig ldflags... 
noninstalled pkgconfig -L /scratch/jiadeng_fluxoe/kojimano/CogMap2/gym/MINOS_Cog_Map_Original/deps/graph-tool-2.26/src/.libs
noninstalled pkgconfig -I /scratch/jiadeng_fluxoe/kojimano/CogMap2/gym/MINOS_Cog_Map_Original/deps/graph-tool-2.26/.
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/graph/Makefile
config.status: creating src/graph/centrality/Makefile
config.status: creating src/graph/clustering/Makefile
config.status: creating src/graph/correlations/Makefile
config.status: creating src/graph/draw/Makefile
config.status: creating src/graph/flow/Makefile
config.status: creating src/graph/generation/Makefile
config.status: creating src/graph/inference/Makefile
config.status: creating src/graph/layout/Makefile
config.status: creating src/graph/search/Makefile
config.status: creating src/graph/spectral/Makefile
config.status: creating src/graph/stats/Makefile
config.status: creating src/graph/topology/Makefile
config.status: creating src/graph/util/Makefile
config.status: creating src/graph_tool/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing graph-tool-py3.5.pc commands
config.status: creating graph-tool-py3.5.pc.in
config.status: creating graph-tool-py3.5.pc
config.status: creating graph-tool-py3.5-uninstalled.pc
config.status: creating graph-tool-py3.5-uninstalled.sh
================================================================================
                             CONFIGURATION SUMMARY                              
================================================================================
Using python version:   3.5.4
Python interpreter:     /home/kojimano/anaconda3/envs/CogMap2/bin/python
Installation path:      /home/kojimano/anaconda3/envs/CogMap2/lib/python3.5/site-packages/graph_tool

C++ compiler (CXX):     /sw/arcts/centos7/gcc/5.4.0/bin/g++ -std=gnu++14
C++ compiler version:   5.4.0

Prefix:                 /home/kojimano/anaconda3/envs/CogMap2/lib
Pkgconfigdir:           ${libdir}/pkgconfig

Python CPP flags:       -I/home/kojimano/anaconda3/envs/CogMap2/include/python3.5m
Python LD flags:        -L/home/kojimano/anaconda3/envs/CogMap2/lib -lpython3.5m
Boost CPP flags:        -pthread -I/include/boost-0
Boost LD flags:         -lboost_iostreams-mt -lboost_python3 -lboost_regex-mt -lboost_context-mt 
Numpy CPP flags:        -I/home/kojimano/anaconda3/envs/CogMap2/lib/python3.5/site-packages/numpy/core/include
Sparsehash CPP flags:   
CGAL CPP flags:         -I/usr/include
CGAL LD flags:          -L/usr/lib -lCGAL -lCGAL_Core -lgmp -lboost_thread -lpthread
Expat CPP flags:        -I/usr/include
Expat LD flags:         -L/usr/lib -lexpat
Cairomm CPP flags:      
Cairomm LD flags:       
OpenMP compiler flags:  -fopenmp
OpenMP LD flags:        
Extra CPPFLAGS:         -DNDEBUG -I/scratch/jiadeng_fluxoe/kojimano/packages/one_six/lib
Extra CXXFLAGS:         -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 
Extra LDFLAGS:          -L/scratch/jiadeng_fluxoe/kojimano/packages/one_six/lib

Using OpenMP:           yes
Using sparsehash:       no
Using cairo:            no
================================================================================
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