October 2014 - graph-tool - archives.skewed.de

Using a EdgePropertyMap('object') as weights
by ambasta 17 Nov '14

17 Nov '14

Hi, I have two problems class Weights: ... g = Graph(directed=True) weights = g.new_edge_property('object') vertex_one = g.add_vertex() vertex_two = g.add_vertex() edge = g.add_edge(vertex_one, vertex_two) weights[edge] = Weights(1) g.shortest_path(vertex_one, vertex_two, weights) This raises ValueError: property map 'dist_map' is not of scalar type. Is there a function I can implement in Weights for it to return a scalar value to be used during calculation of shortest path. Secondly, consider a directed graph where the edge weight is a function of cost at edge's origin vertex, i.e. the weight class is defined as: class Weights: .... def get_weight(current_cost): return self.cost * current_cost Hence during calculation of shortest_path/distance, is it possible to pass the weight at the traversed/visited edge to get the cost of the edge. -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

3 12

Vertex.in_neighbours() throws an error for undirected graphs
by Smith, Steven - 1004 - MITLL 07 Nov '14

07 Nov '14

The Vertex methods in_neighbours() and all_neighbours() throw an error for undirected graphs. Is this behavior intended? Code: > import numpy as np > import numpy.random as rand > import graph_tool.all as gt > > n = 1000; p = 2.0*np.log(n)/n > g = gt.random_graph(n, lambda: rand.poisson((n - 1) * p), directed=False, model="erdos") > v = [v for v in g.vertices() if g.vertex_index[v] == 0][0] > [u.__int__() for u in v.out_neighbours()] > > # Fail: > [u.__int__() for u in v.in_neighbours()] > # Fail: > [u.__int__() for u in v.all_neighbours()] > > # Correct by setting direction > g.is_directed() > g.set_directed(True) > g.is_directed() > [u.__int__() for u in v.in_neighbours()] > [u.__int__() for u in v.out_neighbours()] Error: > File "gt_test.py", line 11, in <module> > [u.__int__() for u in v.in_neighbours()] > File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/__init__.py", line 2327, in _in_neighbours > yield e.source() > ValueError: invalid edge descriptor

2 5

bash: ./configure: No such file or directory
by Assia Az 29 Oct '14

29 Oct '14

Hi everyone, To install graph-tool I've installed the dependencies indicated in: *http://graph-tool.skewed.de/download <http://graph-tool.skewed.de/download>* following those steps: 1/ I downloaded the package: graph-toll-2.2.35.tar.bz2 from the same website. 2/I extracted it in the directory: anaconda/pkgs 3/then I entered those command lines(dependencies): sudo apt-get install GCC sudo apt-get install python sudo apt-get install libboost-all-dev sudo apt-get install expat sudo apt-get install python-SciPy sudo apt-get install python-Numpy sudo apt-get install libcgal-dev sudo apt-get install sparsehash sudo apt-get install libcairomm-1.0 sudo apt-get install libcairomm-1.0-dev sudo apt-get install python-cairo sudo apt-get install python-matplotlib sudo apt-get install graphviz 4/ But when I entered ./configure I had this result: bash: ./configure: No such file or directory I dont know where is the problem? please can you help me...

2 1

Behavior of purge
by Flavien Lambert 29 Oct '14

29 Oct '14

Dear all, I do not understand the behavior of the following code (this is not a minimal example, I tried to reproduce the problem on a minimal example but I could not...). I do not get why, when I purge the vertices and edges after filtering, the properties of the vertices are not consistent. Thanks for your help, Flavien. _graph = gt.Graph(_originalGraph) > > _bus = _graph.new_vertex_property('bool') > _bus.a = True > _trainVertices = [_v for _v in _graph.vertices() if _name[_v][:3] == 'stn'] > > for _v in _trainVertices : > _bus[_v] = False > > print 'original graph #', _graph > print 'train number # ', len([_v for _v in _graph.vertices() if > _name[_v][:3] == 'stn']), '\n' > > > _graph.set_vertex_filter(_bus) > print 'filtered graph #', _graph > print 'train number #', len([_v for _v in _graph.vertices() if > _name[_v][:3] == 'stn']), '\n' > > _graph.purge_vertices() > _graph.purge_edges() > print 'purged graph #', _graph > print 'train number #', len([_v for _v in _graph.vertices() if > _name[_v][:3] == 'stn']), '\n' > original graph # <Graph object, directed, with 2775 vertices and 9341 edges at 0x313be50> > train number # 112 > > filtered graph # <Graph object, directed, with 2663 vertices and 6307 edges, edges filtered by (<PropertyMap object with key type 'Edge' and value type 'bool', for Graph 0x313be50, at 0x2a3c750>, False), vertices filtered by (<PropertyMap object with key type 'Vertex' and value type 'bool', for Graph 0x313be50, at 0x2d62610>, False) at 0x313be50> > train number # 0 > > purged graph # <Graph object, directed, with 2663 vertices and 6307 edges, edges filtered by (<PropertyMap object with key type 'Edge' and value type 'bool', for Graph 0x313be50, at 0x313bc50>, False), vertices filtered by (<PropertyMap object with key type 'Vertex' and value type 'bool', for Graph 0x313be50, at 0x313bb90>, False) at 0x313be50> > train number # 109 > >

2 2

unexpected shortest_path result
by lmz 24 Oct '14

24 Oct '14

Hello -- I am getting an unexpected shortest path (with weighted costs) result. I have isolated it to a simple script to illustrate; the files are at http://www.sfcta.org/downloads/lmz/ Files: - graph: graph_after_1iter_157_277.xml.gz - python script to illustrate my issue: path_debug.py - log file output of python script: path_debug.log The workbook, path_debug.xls, is just an excel version of path_debug.log with a calculated column (in orange) inserted to show what I expect to be the shortest distance to the given vertex. The script path_debug.py: 1) finds the shortest path from a source to a target and prints the details 2) prints the details of what I expect to be the shortest path I cannot figure out why the second path has the cost that it's printing... Mostly it's as expected, but the yellow highlighted cells are what baffles me. The graph is a pseudo-dual network so it's a bit confusing; the vertices symbolize links in a street network and the edges symbolize a turn from the incoming link to the outgoing link. Any help would be greatly appreciated! -Lisa -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

4 6

Getting Started with Graph Tool
by Mike Sherwin 16 Oct '14

16 Oct '14

Hello - I'm just getting started with Graph Tool and was wondering if someone could walk me through the basic set up instructions for either Mac or Windows. Thanks, Mike

2 1

Memory address changing when accessing an edge of the graph
by Guillaume Gay 16 Oct '14

16 Oct '14

Hi all, When manipulating a graph, I create a list of edges with a certain relation to a vertex (they are the edges common to the vertex‘s neighbour). I create this list at some moment in the code, and don’t update it. Later down the execution, I try to remove one of those edges from the list prior to its deletion. That use to work without problem, until today (but I have ran the code since about a month ago). Now when I try to |remove()| the edge, I get a ValueError because python tels me the edge is not in the list. When I look in the list, I see a reference to an edge with the correct source and target, but a different memory address, so I suspect that might be why it can be found… Actually, when accessing an edge form a graph, the edge's address changes: | graph.edge(4747,2693, all_edges=True) [<Edge objectwith source'4747' and target'2693' at0x7fd2d437c048>] graph.edge(4747,2693, all_edges=False) <Edge objectwith source'4747' and target'2693' at0x7fd2d437c0d8> graph.edge(4747,2693, all_edges=False) <Edge objectwith source'4747' and target'2693' at0x7fd2d437c168>| Note the latest digits of the address aren't the same. I see the same kind of things for the vertices, and it produces other bugs down the road (like this one when trying to add an edge between two vertices): |TypeError: No registered converter was able to extract a C++ reference to type graph_tool::PythonVertexfrom this Python object of type NoneType| What is strange is that I can't reproduce the bug in more simple settings, where edge list is created at the same execution level as the call to remove one of those. I seem to recall inspecting the addresses when debugging, to check that my object were consistent, that‘s why it’s strange that they change now. So I'm a bit confused here… Best, Guillaume

2 9

Building a Graph with Repeated Non-Unique Nodes
by tanzairatier 14 Oct '14

14 Oct '14

I'm trying to read data into a graph using Graph-Tool. My code is further below. I'm having the issue of invalid vertex descriptors. Each row in my.data has a start, end, and transition weight. My goal is to iterate through each row, adding the edges (start,end) that have that edge weight of trans. Suppose on the first iteration, my.data has (1,1,2) = (start, trans, end) which is to describe an edge between vertices labeled 1 and 2, with the weight of '1'. Then on the second iteration, suppose my.data has (1,5,3) = (start, trans, end), which is to describe an edge between vertices labeled 1 and 3, with the weight of '5'. Then I'd want a graph with three vertices, 1, 2, 3 and has two edges (1,2) and (1,3). My strategy is to check if a vertex of each label (start,end) exists, and then to add those vertices if they do not exist. The try-catch statements seem to work properly. But when we try to access the added vertices, I get the invalid vertex descriptor (value error) exception. def gtBuildGraph(my): """build a graph using 'Graph-Tool' """ my.graph = gt.Graph() my.weights = my.graph.new_edge_property("int") for row in my.data: start = int(row['start_state']) end = int(row['end_state']) trans = int(row['transition']) #sometimes, start and end nodes are non-unique try: my.graph.vertex(start) except: my.graph.add_vertex(start) try: my.graph.vertex(end) except: my.graph.add_vertex(end) start = my.graph.vertex(start) end = my.graph.vertex(end) newEdge = my.graph.add_edge(start, end) my.weights[newEdge] = trans -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

2 1

Graph-Tool Mac OS Build Errors
by tanzairatier 13 Oct '14

13 Oct '14

I'm attempting to build Graph-Tool on this MacBook Air (OS X 10.9.2). I've got all the dependencies installed, including boost and I've even run tests to confirm boost works. When I run the ./configure and make, I get the error half way into make at graph_correlations.lo. Showing below are the ./configure and make commands. (I've tried with no flags on ./configure and it turned out pretty much the same.) I've also upgraded to gcc48, which got me past a few earlier errors and a little deeper into the files to build through the make command. But I'm stuck here, unsure of what the holdup is. Any help would be appreciated. Thanks! gale:graph-tool tanza$ ./configure CXX=/opt/local/bin/g++-mp-4.8 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking for style of include used by make... GNU 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 whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for library containing strerror... none required checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking whether we are using the GNU C++ compiler... yes checking whether /opt/local/bin/g++-mp-4.8 accepts -g... yes checking dependency style of /opt/local/bin/g++-mp-4.8... gcc3 checking for gcc option to accept ISO C99... unsupported checking for gcc option to accept ISO C89... (cached) none needed checking for gcc option to accept ISO Standard C... (cached) none needed checking how to run the C++ preprocessor... /opt/local/bin/g++-mp-4.8 -E checking for ANSI C header files... (cached) yes checking build system type... x86_64-apple-darwin13.1.0 checking host system type... x86_64-apple-darwin13.1.0 checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /opt/local/bin/ld checking if the linker (/opt/local/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /opt/local/bin/nm checking the name lister (/opt/local/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-apple-darwin13.1.0 file names to x86_64-apple-darwin13.1.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin13.1.0 file names to toolchain format... func_convert_file_noop checking for /opt/local/bin/ld option to reload object files... -r checking for objdump... no checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /opt/local/bin/nm output from gcc object... ok checking for sysroot... no checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/opt/local/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin13.1.0 dyld checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... /opt/local/bin/g++-mp-4.8 -E checking for ld used by /opt/local/bin/g++-mp-4.8... /opt/local/bin/ld checking if the linker (/opt/local/bin/ld) is GNU ld... no checking whether the /opt/local/bin/g++-mp-4.8 linker (/opt/local/bin/ld) supports shared libraries... yes checking for /opt/local/bin/g++-mp-4.8 option to produce PIC... -fno-common -DPIC checking if /opt/local/bin/g++-mp-4.8 PIC flag -fno-common -DPIC works... yes checking if /opt/local/bin/g++-mp-4.8 static flag -static works... no checking if /opt/local/bin/g++-mp-4.8 supports -c -o file.o... yes checking if /opt/local/bin/g++-mp-4.8 supports -c -o file.o... (cached) yes checking whether the /opt/local/bin/g++-mp-4.8 linker (/opt/local/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin13.1.0 dyld checking how to hardcode library paths into programs... immediate checking target system type... x86_64-apple-darwin13.1.0 checking whether to enable debug info...... no checking whether C++ compiler supports -std=gnu++11... yes checking whether to enable function inlining...... yes checking whether to enable optimizations...... yes checking whether to enable symbol visibility manipulation...... yes checking whether to enable parallel algorithms with openmp...... no checking whether to enable cairo drawing...... yes checking for main in -lm... yes checking for main in -lbz2... yes checking for main in -lexpat... yes ================ Detecting python ================ checking for a Python interpreter with version >= 2.6... python checking for python... /usr/bin/python checking for python version... 2.7 checking for python platform... darwin checking for python script directory... ${prefix}/lib/python2.7/site-packages checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-packages checking for python2.7... (cached) /usr/bin/python checking for a version of Python >= '2.1.0'... yes checking for a version of Python == '2.7.5'... yes checking for the distutils Python package... yes checking for Python include path... -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 checking for Python library path... -L/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/config -lpython2.7 checking for Python site-packages path... /Library/Python/2.7/site-packages checking python extra libraries... -ldl -framework CoreFoundation checking python extra linking flags... -u _PyMac_Error /System/Library/Frameworks/Python.framework/Versions/2.7/Python checking consistency of all components of python development environment... yes graph-tool will be installed at: /Library/Python/2.7/site-packages =========================== Using python version: 2.7.5 =========================== checking for boostlib >= 1.38.0... yes checking whether the Boost::Python library is available... yes checking for exit in -lboost_python... yes checking whether the Boost::Iostreams library is available... yes checking for exit in -lboost_iostreams... yes checking whether the Boost::Regex library is available... yes checking for exit in -lboost_regex... yes checking whether the Boost::Graph library is available... yes checking for exit in -lboost_graph... yes checking for main in -lCGAL... yes checking whether to cgal debbuging with valgrind...... no checking python module: numpy... yes checking for /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/arrayobject.h... yes checking python module: scipy... yes checking /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy/weave/scxx/object.h usability... yes checking /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy/weave/scxx/object.h presence... yes checking for /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy/weave/scxx/object.h... yes checking expat.h usability... yes checking expat.h presence... yes checking for expat.h... yes checking CGAL/version.h usability... yes checking CGAL/version.h presence... yes checking for CGAL/version.h... yes checking for pkg-config... /opt/local/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for CAIROMM... yes checking python module: cairo... no checking pycairo/pycairo.h usability... yes checking pycairo/pycairo.h presence... yes checking for pycairo/pycairo.h... yes checking whether to enable sparsehash...... yes checking for SPARSEHASH... yes checking sparsehash/dense_hash_set usability... yes checking sparsehash/dense_hash_set presence... yes checking for sparsehash/dense_hash_set... yes 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/community/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/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: executing depfiles commands config.status: executing libtool commands configure: Modifying libtool to correctly link libstdc++ before anything else... gale:graph-tool tanza$ make /Library/Developer/CommandLineTools/usr/bin/make all-recursive Making all in src Making all in graph Making all in centrality CXX graph_betweenness.lo CXX graph_closeness.lo CXX graph_eigentrust.lo CXX graph_eigenvector.lo CXX graph_hits.lo CXX graph_katz.lo CXX graph_pagerank.lo CXX graph_trust_transitivity.lo CXXLD libgraph_tool_centrality.la Making all in clustering CXX graph_clustering.lo CXX graph_extended_clustering.lo CXX graph_motifs.lo CXXLD libgraph_tool_clustering.la Making all in community CXX graph_blockmodel.lo CXX graph_community.lo CXX graph_community_network.lo CXX graph_community_network_edges.lo CXX graph_community_network_vavg.lo CXX graph_community_network_eavg.lo CXX graph_community_network_eavg_imp1.lo CXXLD libgraph_tool_community.la Making all in correlations CXX graph_assortativity.lo CXX graph_correlations.lo In file included from ./../numpy_bind.hh:33:0, from graph_correlations.hh:28, from graph_corr_hist.hh:21, from graph_correlations.cc:27: ./../numpy_bind_old.hh: In instantiation of 'boost::python::api::object wrap_vector_owned(std::vector<_RealType>&) [with ValueType = long unsigned int]': graph_corr_hist.hh:76:50: required from 'void graph_tool::get_correlation_histogram<GetDegreePair>::operator()(Graph&, DegreeSelector1, DegreeSelector2, WeightMap) const [with Graph = boost::adj_list<long unsigned int>; DegreeSelector1 = graph_tool::in_degreeS; DegreeSelector2 = graph_tool::in_degreeS; WeightMap = graph_tool::ConstantPropertyMap<int, boost::adj_list<long unsigned int>::edge_descriptor>; GetDegreePair = graph_tool::GetNeighboursPairs]' ./../graph_filtering.hh:463:9: required from 'void graph_tool::detail::action_wrap<Action, Wrap>::operator()(T1*, Ts&& ...) const [with T1 = boost::adj_list<long unsigned int>; Ts = {graph_tool::in_degreeS&, graph_tool::in_degreeS&, graph_tool::ConstantPropertyMap<int, boost::adj_list<long unsigned int>::edge_descriptor>&}; Action = graph_tool::get_correlation_histogram<graph_tool::GetNeighboursPairs>; Wrap = mpl_::bool_<false>]' ./../mpl_nested_loop.hh:174:9: required from 'void boost::mpl::selected_types<Action>::dispatch(unsigned int, std::tuple<>, Args&& ...) const [with Args = {boost::adj_list<long unsigned int>*&, graph_tool::in_degreeS&, graph_tool::in_degreeS&, graph_tool::ConstantPropertyMap<int, boost::adj_list<long unsigned int>::edge_descriptor>&}; Action = graph_tool::detail::action_wrap<graph_tool::get_correlation_histogram<graph_tool::GetNeighboursPairs>, mpl_::bool_<false> >]' ./../mpl_nested_loop.hh:168:81: [ skipping 19 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] ./../mpl_nested_loop.hh:100:48: required from 'void boost::mpl::nested_for_each_imp(Action) [with TR1 = graph_tool::scalar_selectors; TRS = {graph_tool::scalar_selectors, boost::mpl::vector<graph_tool::ConstantPropertyMap<int, boost::adj_list<long unsigned int>::edge_descriptor>, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>}; Action = boost::mpl::dispatch<boost::mpl::selected_types<graph_tool::detail::action_wrap<graph_tool::get_correlation_histogram<graph_tool::GetNeighboursPairs>, mpl_::bool_<false> > >, boost::adj_list<long unsigned int>*>]' ./../mpl_nested_loop.hh:91:49: required from 'void boost::mpl::inner_loop<Action, TRS>::operator()(T) const [with T = boost::adj_list<long unsigned int>*; Action = boost::mpl::dispatch<boost::mpl::selected_types<graph_tool::detail::action_wrap<graph_tool::get_correlation_histogram<graph_tool::GetNeighboursPairs>, mpl_::bool_<false> > > >; TRS = {graph_tool::scalar_selectors, graph_tool::scalar_selectors, boost::mpl::vector<graph_tool::ConstantPropertyMap<int, boost::adj_list<long unsigned int>::edge_descriptor>, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>}]' /usr/local/include/boost/mpl/for_each.hpp:78:25: required from 'static void boost::mpl::aux::for_each_impl<false>::execute(Iterator*, LastIterator*, TransformFunc*, F) [with Iterator = boost::mpl::v_iter<graph_tool::detail::graph_action<graph_tool::get_correlation_histogram<graph_tool::GetNeighboursPairs>, graph_tool::detail::all_graph_views, mpl_::bool_<false>, graph_tool::scalar_selectors, graph_tool::scalar_selectors, boost::mpl::vector<graph_tool::ConstantPropertyMap<int, boost::adj_list<long unsigned int>::edge_descriptor>, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na> >::graph_view_pointers, 0l>; LastIterator = boost::mpl::v_iter<graph_tool::detail::graph_action<graph_tool::get_correlation_histogram<graph_tool::GetNeighboursPairs>, graph_tool::detail::all_graph_views, mpl_::bool_<false>, graph_tool::scalar_selectors, graph_tool::scalar_selectors, boost::mpl::vector<graph_tool::ConstantPropertyMap<int, boost::adj_list<long unsigned int>::edge_descriptor>, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na> >::graph_view_pointers, 6l>; TransformFunc = boost::mpl::identity<mpl_::na>; F = boost::mpl::inner_loop<boost::mpl::dispatch<boost::mpl::selected_types<graph_tool::detail::action_wrap<graph_tool::get_correlation_histogram<graph_tool::GetNeighboursPairs>, mpl_::bool_<false> > > >, graph_tool::scalar_selectors, graph_tool::scalar_selectors, boost::mpl::vector<graph_tool::ConstantPropertyMap<int, boost::adj_list<long unsigned int>::edge_descriptor>, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na> >]' /usr/local/include/boost/mpl/for_each.hpp:105:97: required from 'void boost::mpl::for_each(F, Sequence*, TransformOp*) [with Sequence = graph_tool::detail::graph_action<graph_tool::get_correlation_histogram<graph_tool::GetNeighboursPairs>, graph_tool::detail::all_graph_views, mpl_::bool_<false>, graph_tool::scalar_selectors, graph_tool::scalar_selectors, boost::mpl::vector<graph_tool::ConstantPropertyMap<int, boost::adj_list<long unsigned int>::edge_descriptor>, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na> >::graph_view_pointers; TransformOp = boost::mpl::identity<mpl_::na>; F = boost::mpl::inner_loop<boost::mpl::dispatch<boost::mpl::selected_types<graph_tool::detail::action_wrap<graph_tool::get_correlation_histogram<graph_tool::GetNeighboursPairs>, mpl_::bool_<false> > > >, graph_tool::scalar_selectors, graph_tool::scalar_selectors, boost::mpl::vector<graph_tool::ConstantPropertyMap<int, boost::adj_list<long unsigned int>::edge_descriptor>, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na> >]' /usr/local/include/boost/mpl/for_each.hpp:118:48: required from 'void boost::mpl::for_each(F, Sequence*) [with Sequence = graph_tool::detail::graph_action<graph_tool::get_correlation_histogram<graph_tool::GetNeighboursPairs>, graph_tool::detail::all_graph_views, mpl_::bool_<false>, graph_tool::scalar_selectors, graph_tool::scalar_selectors, boost::mpl::vector<graph_tool::ConstantPropertyMap<int, boost::adj_list<long unsigned int>::edge_descriptor>, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na> >::graph_view_pointers; F = boost::mpl::inner_loop<boost::mpl::dispatch<boost::mpl::selected_types<graph_tool::detail::action_wrap<graph_tool::get_correlation_histogram<graph_tool::GetNeighboursPairs>, mpl_::bool_<false> > > >, graph_tool::scalar_selectors, graph_tool::scalar_selectors, boost::mpl::vector<graph_tool::ConstantPropertyMap<int, boost::adj_list<long unsigned int>::edge_descriptor>, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na> >]' ./../mpl_nested_loop.hh:100:48: required from 'void boost::mpl::nested_for_each_imp(Action) [with TR1 = graph_tool::detail::graph_action<graph_tool::get_correlation_histogram<graph_tool::GetNeighboursPairs>, graph_tool::detail::all_graph_views, mpl_::bool_<false>, graph_tool::scalar_selectors, graph_tool::scalar_selectors, boost::mpl::vector<graph_tool::ConstantPropertyMap<int, boost::adj_list<long unsigned int>::edge_descriptor>, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na> >::graph_view_pointers; TRS = {graph_tool::scalar_selectors, graph_tool::scalar_selectors, boost::mpl::vector<graph_tool::ConstantPropertyMap<int, boost::adj_list<long unsigned int>::edge_descriptor>, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>}; Action = boost::mpl::dispatch<boost::mpl::selected_types<graph_tool::detail::action_wrap<graph_tool::get_correlation_histogram<graph_tool::GetNeighboursPairs>, mpl_::bool_<false> > > >]' ./../mpl_nested_loop.hh:113:34: required from 'void boost::mpl::nested_for_each(Action) [with TRS = {graph_tool::detail::graph_action<graph_tool::get_correlation_histogram<graph_tool::GetNeighboursPairs>, graph_tool::detail::all_graph_views, mpl_::bool_<false>, graph_tool::scalar_selectors, graph_tool::scalar_selectors, boost::mpl::vector<graph_tool::ConstantPropertyMap<int, boost::adj_list<long unsigned int>::edge_descriptor>, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na> >::graph_view_pointers, graph_tool::scalar_selectors, graph_tool::scalar_selectors, boost::mpl::vector<graph_tool::ConstantPropertyMap<int, boost::adj_list<long unsigned int>::edge_descriptor>, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>}; Action = boost::mpl::selected_types<graph_tool::detail::action_wrap<graph_tool::get_correlation_histogram<graph_tool::GetNeighboursPairs>, mpl_::bool_<false> > >]' ./../graph_filtering.hh:490:85: required from 'void graph_tool::detail::graph_action<Action, GraphViews, Wrap, TRS>::operator()(Args&& ...) const [with Args = {boost::any, boost::any, boost::any&}; Action = graph_tool::get_correlation_histogram<graph_tool::GetNeighboursPairs>; GraphViews = graph_tool::detail::all_graph_views; Wrap = mpl_::bool_<false>; TRS = {graph_tool::scalar_selectors, graph_tool::scalar_selectors, boost::mpl::vector<graph_tool::ConstantPropertyMap<int, boost::adj_list<long unsigned int>::edge_descriptor>, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>}]' graph_correlations.cc:78:71: required from here ./../numpy_bind_old.hh:58:65: error: 'value' is not a member of 'boost::mpl::aux::wrapped_type<boost::mpl::aux::type_wrapper<mpl_::void_> >::type {aka mpl_::void_}' int val_type = boost::mpl::at<numpy_types,ValueType>::type::value; ^ make[4]: *** [graph_correlations.lo] Error 1 make[3]: *** [all-recursive] Error 1 make[2]: *** [all-recursive] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2 -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

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installation: make fails at graph_blockmodel_overlap.hh
by Ács Judit 03 Oct '14

03 Oct '14

Hi, I have been trying to install graph-tool on a Debian server which I don't have root access for for a day now, and after some of trouble I was able to run configure but now make fails with the following: CXX graph_blockmodel.lo In file included from graph_blockmodel.cc:39:0: graph_blockmodel_overlap.hh: In lambda function: graph_blockmodel_overlap.hh:900:50: error: no match for ‘operator[]’ in ‘((graph_tool::overlap_partition_stats_t*)this)->graph_tool::overlap_partition_stats_t::_embhist[bv_i]’ graph_blockmodel_overlap.hh:900:50: note: candidates are: In file included from /usr/include/c++/4.7/bits/hashtable.h:36:0, from /usr/include/c++/4.7/unordered_set:45, from ./../graph_properties.hh:24, from ./../graph.hh:35, from ./../graph_filtering.hh:21, from graph_blockmodel.cc:28: /usr/include/c++/4.7/bits/hashtable_policy.h:435:5: note: std::__detail::_Map_base<_Key, _Pair, std::_Select1st<_Pair>, true, _Hashtable>::mapped_type& std::__detail::_Map_base<_Key, _Pair, std::_Select1st<_Pair>, true, _Hashtable>::operator[](const _Key&) [with _Key = std::vector<int>; _Pair = std::pair<const std::vector<int>, std::vector<long unsigned int> >; _Hashtable = std::_Hashtable<std::vector<int>, std::pair<const std::vector<int>, std::vector<long unsigned int> >, std::allocator<std::pair<const std::vector<int>, std::vector<long unsigned int> > >, std::_Select1st<std::pair<const std::vector<int>, std::vector<long unsigned int> > >, std::equal_to<std::vector<int> >, std::hash<std::vector<int> >, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, true, false, true>; std::__detail::_Map_base<_Key, _Pair, std::_Select1st<_Pair>, true, _Hashtable>::mapped_type = std::vector<long unsigned int>] <near match> /usr/include/c++/4.7/bits/hashtable_policy.h:435:5: note: no known conversion for implicit ‘this’ parameter from ‘const ebhist_t* {aka const std::unordered_map<std::vector<int>, std::vector<long unsigned int> >*}’ to ‘std::__detail::_Map_base<std::vector<int>, std::pair<const std::vector<int>, std::vector<long unsigned int> >, std::_Select1st<std::pair<const std::vector<int>, std::vector<long unsigned int> > >, true, std::_Hashtable<std::vector<int>, std::pair<const std::vector<int>, std::vector<long unsigned int> >, std::allocator<std::pair<const std::vector<int>, std::vector<long unsigned int> > >, std::_Select1st<std::pair<const std::vector<int>, std::vector<long unsigned int> > >, std::equal_to<std::vector<int> >, std::hash<std::vector<int> >, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, true, false, true> >*’ This goes on for several lines. Am I using the wrong compiler? My gcc version is 4.7.2. I read the INSTALL file and I can't find the solution. I disabled cairo and sparsehash. Do you have any idea why I'm getting these errors? Thanks, Judit Ács

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