graph-tool November 2014

graph-tool@skewed.de

13 participants
25 discussions

Fail to 'make' in OSX
by munddr 09 Nov '14

09 Nov '14

Hi I'm trying to compile the source. I *believe* I already have all of the dependencies installed (via brew and pip), but when I run 'make', I get the following errors: ... ./../numpy_bind_old.hh:56:23: note: candidate template ignored: substitution failure [with ValueType = unsigned long] boost::python::object wrap_vector_owned(vector<ValueType>& vec) ^ In file included from graph_correlations.cc:27: ./graph_corr_hist.hh:77:25: error: no matching function for call to 'wrap_vector_owned' ret_bins.append(wrap_vector_owned(bins[1])); ^~~~~~~~~~~~~~~~~ ./../numpy_bind_old.hh:56:23: note: candidate template ignored: substitution failure [with ValueType = unsigned long] boost::python::object wrap_vector_owned(vector<ValueType>& vec) ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 2 warnings and 20 errors generated. 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 Does anyone know what might be wrong or missing? Thanks a lot in advance. John -- 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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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

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Error building graph-tool against Boost 1.53 on Ubuntu 12.04 x86-64 and g++-4.6.3
by linello 05 Nov '14

05 Nov '14

I'm trying to build graph-tool but can't figure out how to solve a compilation error that I get everytime. I think it is related to a bug in Boost, but I have downloaded and compiled the latest Boost (1.57) in a staged folder in home Here are my specs: 1) Downloaded and extracted Boost 1.53 in my home folder 2) Compiled Boost in ~/boost_1_53_0 3) Checked that is working fine, when linking against other projects I have. 4) Downloaded graph-tool 2.2.35 in ~/graph-tool-2.2.35 5) export BOOST_ROOT=~/boost_1_57_0/ 5) ./configure --with-boost=$BOOST_ROOT 6) Configuration OK! 7) make And I'm stuck with this error: graph_subgraph_isomorphism.cc:106:17: error: 'vf2_subgraph_mono' was not declared in this scope As well as many other errors. So I've changed boost to the latest 1.57 and a plenty of other errors appears, in particular this error appeared that seems to be unsolvable. http://stackoverflow.com/questions/25395805/compile-error-with-boost-graph-… Now the question is: what is a suitable configuration of Boost and compiler on Ubuntu 12.04 in order to compile graph-tool? -- 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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Graph tool configure error in linux centos
by researcher 05 Nov '14

05 Nov '14

In order to install Graph-tool graph-tool-2.2.35, I have first installed pythons 3.2 and C++ boost library boost_1_56_0. However when I run ./configure for graph tool. I got the following error: checking for Python library path... -L/usr/local/lib -lpython3.2m checking for Python site-packages path... /usr/local/lib/python3.2/site-packages checking python extra libraries... -lpthread -ldl -lutil -lm checking python extra linking flags... -Xlinker -export-dynamic checking consistency of all components of python development environment... yes graph-tool will be installed at: /usr/local/lib/python3.2/site-packages =========================== Using python version: 3.2.6 =========================== checking for boostlib >= 1.53.0... yes checking whether the Boost::Python library is available... ./configure: line 17408: test: too many arguments yes checking for exit in -lboost_python... no checking for exit in -lboost_python... (cached) no checking for exit in -lboost_python... (cached) no checking for exit in -lboost_python... (cached) no checking for exit in -lboost_python... (cached) no checking for exit in -lboost_python... (cached) no configure: error: No usable boost::python found My boost installation is under= /var/boost_1_56_0 boost library= /var/myboost GraphTool= /mnt/data/home/foo/graphtool/graph-tool-2.2.35 Python= /mnt/data/home/foo/graphtool/Python-3.2.6 Can you please help me out How can I fix this issue? -- 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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Boost C++ library Version Issue
by researcher 04 Nov '14

04 Nov '14

Hi After downloading and untar the file "boost_1_56_0.tar.gz", I have installed Boost C++ library version "boost_1_56_0" in linux centos, I have run the following command to install. sudo ./bootstrap.sh --prefix=/usr/local sudo ./b2 install. It has been successfully installed. However when I checked the version it showed different version $ cat /usr/include/boost/version.hpp | grep "BOOST_LIB_VERSION" #define BOOST_LIB_VERSION "1_33_1" I have tried to install boost_1_55_0 as well in another folder but unfortunately still it shows version 1_33_1. Can anyone here tell me how I can fix it. Because of this issue I am unsuccessfull to configure Graph_tool that shows following error: checking for boostlib >= 1.53.0... configure: error: We could not detect the boost libraries (version 1.53 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. Your help in this regrad would highly be appreciated -- 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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graph-tool November 2014