graph-tool May 2018

graph-tool@skewed.de

4 participants
13 discussions

Error during make
by P-M 12 Jun '18

12 Jun '18

Hello, I am trying to compile the git version of graph-tool. I have configured it as follows: ./configure --with-boost=/opt/anaconda/anaconda3 --enable-openmp This returns a configuration summary as follows: ================================================================================ CONFIGURATION SUMMARY ================================================================================ Using python version: 2.7.14 Python interpreter: /opt/anaconda/anaconda3/bin/python Installation path: /opt/anaconda/anaconda3/lib/python2.7/site-packages/graph_tool C++ compiler (CXX): g++ -std=gnu++14 C++ compiler version: 5.4.0 Prefix: /usr/local Pkgconfigdir: ${libdir}/pkgconfig Python CPP flags: -I/opt/anaconda/anaconda3/include/python2.7 Python LD flags: -L/opt/anaconda/anaconda3/lib -lpython2.7 Boost CPP flags: -pthread -I/opt/anaconda/anaconda3/include Boost LD flags: -lboost_iostreams -lboost_python -lboost_regex -lboost_context -lboost_coroutine Numpy CPP flags: -I/opt/anaconda/anaconda3/lib/python2.7/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: -I/usr/include/cairomm-1.0 -I/usr/lib/x86_64-linux-gnu/cairomm-1.0/include -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/sigc++-2.0 -I/usr/lib/x86_64-linux-gnu/sigc++-2.0/include Cairomm LD flags: -lcairomm-1.0 -lcairo -lsigc-2.0 OpenMP compiler flags: -fopenmp OpenMP LD flags: Extra CPPFLAGS: -DNDEBUG Extra CXXFLAGS: -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0 Extra LDFLAGS: Using OpenMP: yes Using sparsehash: yes Using cairo: yes ================================================================================ and the following config.log config.log <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> . I then have run make -j20 This seems to fail with the following output make -j20 make all-recursive make[1]: Entering directory '/home/pmj27/graph-tool' Making all in src make[2]: Entering directory '/home/pmj27/graph-tool/src' Making all in graph make[3]: Entering directory '/home/pmj27/graph-tool/src/graph' Making all in centrality make[4]: Entering directory '/home/pmj27/graph-tool/src/graph/centrality' CXX graph_betweenness.lo CXX graph_centrality_bind.lo CXX graph_closeness.lo CXX graph_eigenvector.lo CXX graph_hits.lo CXX graph_eigentrust.lo CXX graph_pagerank.lo CXX graph_katz.lo CXX graph_trust_transitivity.lo CXXLD libgraph_tool_centrality.la make[4]: Leaving directory '/home/pmj27/graph-tool/src/graph/centrality' Making all in clustering make[4]: Entering directory '/home/pmj27/graph-tool/src/graph/clustering' CXX graph_clustering.lo CXX graph_extended_clustering.lo CXX graph_motifs.lo CXXLD libgraph_tool_clustering.la make[4]: Leaving directory '/home/pmj27/graph-tool/src/graph/clustering' Making all in correlations make[4]: Entering directory '/home/pmj27/graph-tool/src/graph/correlations' CXX graph_assortativity.lo CXX graph_correlations.lo CXX graph_correlations_imp1.lo CXX graph_correlations_bind.lo CXX graph_correlations_combined.lo CXX graph_avg_correlations.lo CXX graph_avg_correlations_imp1.lo CXX graph_avg_correlations_combined.lo In file included from /opt/anaconda/anaconda3/include/boost/multi_array.hpp:26:0, from ../../../src/graph/histogram.hh:26, from graph_correlations.hh:27, from graph_avg_correlations.hh:21, from graph_avg_correlations_combined.cc:26: /opt/anaconda/anaconda3/include/boost/multi_array/base.hpp: In member function ‘boost::multi_array<T, NumDims, Allocator>& boost::multi_array<T, NumDims, Allocator>::resize(const boost::detail::multi_array::extent_gen<NumDims>&) [with T = double; long unsigned int NumDims = 1ul; Allocator = std::allocator<double>]’: /opt/anaconda/anaconda3/include/boost/multi_array/base.hpp:416:31: warning: ‘new_strides.boost::array<long int, 1ul>::elems[0ul]’ may be used uninitialized in this function [-Wmaybe-uninitialized] boost::array<index,NDims> new_strides; ^ /opt/anaconda/anaconda3/include/boost/multi_array/base.hpp: In member function ‘boost::multi_array<T, NumDims, Allocator>& boost::multi_array<T, NumDims, Allocator>::resize(const boost::detail::multi_array::extent_gen<NumDims>&) [with T = int; long unsigned int NumDims = 1ul; Allocator = std::allocator<int>]’: /opt/anaconda/anaconda3/include/boost/multi_array/base.hpp:416:31: warning: ‘new_strides.boost::array<long int, 1ul>::elems[0ul]’ may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from /opt/anaconda/anaconda3/include/boost/multi_array.hpp:26:0, from ../../../src/graph/histogram.hh:26, from graph_correlations.hh:27, from graph_avg_correlations.hh:21, from graph_avg_correlations.cc:26: /opt/anaconda/anaconda3/include/boost/multi_array/base.hpp: In member function ‘boost::multi_array<T, NumDims, Allocator>& boost::multi_array<T, NumDims, Allocator>::resize(const boost::detail::multi_array::extent_gen<NumDims>&) [with T = double; long unsigned int NumDims = 1ul; Allocator = std::allocator<double>]’: /opt/anaconda/anaconda3/include/boost/multi_array/base.hpp:416:31: warning: ‘new_strides.boost::array<long int, 1ul>::elems[0ul]’ may be used uninitialized in this function [-Wmaybe-uninitialized] boost::array<index,NDims> new_strides; ^ /opt/anaconda/anaconda3/include/boost/multi_array/base.hpp: In member function ‘boost::multi_array<T, NumDims, Allocator>& boost::multi_array<T, NumDims, Allocator>::resize(const boost::detail::multi_array::extent_gen<NumDims>&) [with T = int; long unsigned int NumDims = 1ul; Allocator = std::allocator<int>]’: /opt/anaconda/anaconda3/include/boost/multi_array/base.hpp:416:31: warning: ‘new_strides.boost::array<long int, 1ul>::elems[0ul]’ may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from /opt/anaconda/anaconda3/include/boost/multi_array.hpp:26:0, from ../../../src/graph/histogram.hh:26, from graph_avg_correlations_imp1.cc:21: /opt/anaconda/anaconda3/include/boost/multi_array/base.hpp: In member function ‘boost::multi_array<T, NumDims, Allocator>& boost::multi_array<T, NumDims, Allocator>::resize(const boost::detail::multi_array::extent_gen<NumDims>&) [with T = double; long unsigned int NumDims = 1ul; Allocator = std::allocator<double>]’: /opt/anaconda/anaconda3/include/boost/multi_array/base.hpp:416:31: warning: ‘new_strides.boost::array<long int, 1ul>::elems[0ul]’ may be used uninitialized in this function [-Wmaybe-uninitialized] boost::array<index,NDims> new_strides; ^ /opt/anaconda/anaconda3/include/boost/multi_array/base.hpp: In member function ‘boost::multi_array<T, NumDims, Allocator>& boost::multi_array<T, NumDims, Allocator>::resize(const boost::detail::multi_array::extent_gen<NumDims>&) [with T = long double; long unsigned int NumDims = 1ul; Allocator = std::allocator<long double>]’: /opt/anaconda/anaconda3/include/boost/multi_array/base.hpp:416:31: warning: ‘new_strides.boost::array<long int, 1ul>::elems[0ul]’ may be used uninitialized in this function [-Wmaybe-uninitialized] /opt/anaconda/anaconda3/include/boost/multi_array/base.hpp: In member function ‘boost::multi_array<T, NumDims, Allocator>& boost::multi_array<T, NumDims, Allocator>::resize(const boost::detail::multi_array::extent_gen<NumDims>&) [with T = long double; long unsigned int NumDims = 1ul; Allocator = std::allocator<long double>]’: /opt/anaconda/anaconda3/include/boost/multi_array/base.hpp:416:31: warning: ‘new_strides.boost::array<long int, 1ul>::elems[0ul]’ may be used uninitialized in this function [-Wmaybe-uninitialized] /opt/anaconda/anaconda3/include/boost/multi_array/base.hpp: In member function ‘boost::multi_array<T, NumDims, Allocator>& boost::multi_array<T, NumDims, Allocator>::resize(const boost::detail::multi_array::extent_gen<NumDims>&) [with T = long double; long unsigned int NumDims = 1ul; Allocator = std::allocator<long double>]’: /opt/anaconda/anaconda3/include/boost/multi_array/base.hpp:416:31: warning: ‘new_strides.boost::array<long int, 1ul>::elems[0ul]’ may be used uninitialized in this function [-Wmaybe-uninitialized] CXXLD libgraph_tool_correlations.la make[4]: Leaving directory '/home/pmj27/graph-tool/src/graph/correlations' Making all in draw make[4]: Entering directory '/home/pmj27/graph-tool/src/graph/draw' CXX graph_cairo_draw.lo CXX graph_tree_cts.lo CXX pycairo_aux.lo In file included from pycairo_aux.cc:20:0: pycairo_aux.cc: In function ‘PyObject* gt_PycairoContext_FromContext(cairo_t*, PyTypeObject*, PyObject*)’: /opt/anaconda/anaconda3/include/pycairo/pycairo.h:171:39: error: ‘Pycairo_CAPI’ was not declared in this scope #define PycairoContext_FromContext (Pycairo_CAPI->Context_FromContext) ^ pycairo_aux.cc:26:12: note: in expansion of macro ‘PycairoContext_FromContext’ return PycairoContext_FromContext(ctx, type, base); ^ Makefile:575: recipe for target 'pycairo_aux.lo' failed make[4]: *** [pycairo_aux.lo] Error 1 make[4]: *** Waiting for unfinished jobs.... make[4]: Leaving directory '/home/pmj27/graph-tool/src/graph/draw' Makefile:753: recipe for target 'all-recursive' failed make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory '/home/pmj27/graph-tool/src/graph' Makefile:423: recipe for target 'all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory '/home/pmj27/graph-tool/src' Makefile:595: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/home/pmj27/graph-tool' Makefile:482: recipe for target 'all' failed make: *** [all] Error 2 Could somebody help me identify where I am going wrong? I am running Ubuntu 16.04 and python2.7 (Anaconda). Best, Philipp -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Posterior entropy approximations = 0?
by P-M 23 May '18

23 May '18

Hello, I am sampling the posterior distribution in order to carry out some model selection (much like outlined in the cookbook). Interestingly both the Bethe as well as the mean field approximations of the posterior entropy appear to be returning an answer of 0.0. I was thus after some opinions: Are there cases where I might reasonably expect this to be the correct answer/how would people check that it is not simply being caused by the approximations not being applicable to my data set? Thank you for any help in advance! -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

2 5

boost dependencies while installing gt on Ubuntu 18.04
by Snehal Shekatkar 01 May '18

01 May '18

Hello Tiago, I am trying to install graph-tool on Ubuntu 18.04. I am encountering problems related to boost. What could be done? Reading package lists... Done Building dependency tree Reading state information... Done Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: python-graph-tool : Depends: libboost-graph1.65.0 but it is not installable Depends: libboost-iostreams1.65.0 but it is not installable Depends: libboost-python1.65.0 but it is not installable Depends: libboost-system1.65.0 but it is not installable Depends: libboost-thread1.65.0 but it is not installable Depends: libboost-regex1.65.0 but it is not installable Depends: libcgal12 but it is not installable E: Unable to correct problems, you have held broken packages. Sent with [ProtonMail](https://protonmail.com) Secure Email.

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graph-tool May 2018