March 2017 - graph-tool - archives.skewed.de

apt-get fail to download index files
by Andy Maloney 10 Mar '17

10 Mar '17

I am trying to install graph-tool on a Trusty Ubuntu virtualbox being hosted on a Mac. I've added the requisite lines deb http://downloads.skewed.de/apt/trusty trusty main deb-src http://downloads.skewed.de/apt/trusty trusty main to my /etc/apt/sources.list, but when I run a sudo apt-get update, I get the following errors: W: Failed to fetch http://downloads.skewed.de/apt/trusty/dists/trusty/Release Unable to find expected entry 'main/source/Sources' in Release file (Wrong sources.list entry or malformed file) E: Some index files failed to download. They have been ignored, or old ones used instead. I have the main, universe, and multiverse repositories available. If any one has come across this problem before, please let me know how to fix it. Thanks. Andy_

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Anaconda looking for libicui18n.so.56 despite only version 54.1 being installed
by P-M 09 Mar '17

09 Mar '17

I am trying to compile graph-tool on a machine of mine (Ubuntu 16.04, boost 1.60.0 and gcc 5.4.0) . To do this I am using ./configure CXXFLAGS="-std=gnu++14 -Wno-unused-local-typedefs" PYTHON="/home/pmj27/anaconda2/bin/python2.7" --enable-openmp --with-boost=/home/pmj27/anaconda2 When importing graph_tool.all in python, however, I get an error message as follows: Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/pmj27/anaconda2/lib/python2.7/site-packages/graph_tool/__init__.py", line 111, in <module> dl_import("from . import libgraph_tool_core as libcore") File "/home/pmj27/anaconda2/lib/python2.7/site-packages/graph_tool/dl_import.py", line 61, in dl_import exec(import_expr, local_dict, global_dict) File "<string>", line 1, in <module> ImportError: libicui18n.so.56: cannot open shared object file: No such file or directory Checking for the location of `libicui18n.so` (/home/pmj27/anaconda2/lib) I have tried ./configure CXXFLAGS="-std=gnu++14 -Wno-unused-local-typedefs" PYTHON="/home/pmj27/anaconda2/bin/python2.7" LDFLAGS="-L/home/pmj27/anaconda2/lib" --enable-openmp --with-boost=/home/pmj27/anaconda2 this however returns the same error. Checking `conda list` the icu version that is running is indeed only version 54.1 so I am not surprised that it cannot pick up version 56. I am wondering though why it is looking for version 56 in the first place. My suspicion is that this may be an anaconda issue introduced by some package but am not 100% sure. If it is an anaconda issue how would I go about tracking down which package is causing it to try and import libicui18n.so.56 so that I can see if there is a fix for it? -- 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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eweight vs. recs in BlockState
by Peter Straka 08 Mar '17

08 Mar '17

Dear list, what exactly does the 'recs' (and rec_types) parameter in 'BlockState' and 'LayeredBlockState' do? I couldn't find an example in the documentation. But for instance if I have a network with integer edge weights (stored in the PropertyMap 'weight'), I could specify recs=[weight], rec_types=["discrete-poisson"]. And probably that would assume a Poisson distribution for the weights; am I right? If I am, then would this be the same as specifying eweight=weight and deg_corr=False? Many thanks in advance, Peter

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Building error on CentOS 6.8; ‘CoroGenerator’ was not declared in this scope
by vanmil 06 Mar '17

06 Mar '17

Hi all, I'm experiencing the following error when trying to build graph-tool for CentOS 6.8. I am building graph tool on a docker image with the following configuration. As can be seen in the following code running the configuration with Dockerfile: Already survived a lot of installation errors (because I know CentOS is not the easiest platform to build for, but required to use it.), but I can't find a solution to this error online and do not have enough knowledge of the configuration error to solve it myself. I you could help me out I would greatly appreciate it! Thanks in advance, Jelle -- 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.Python.ArgumentError: Python argument types did not match C++ signature
by P-M 03 Mar '17

03 Mar '17

I have been trying to compile the recent git version of graph-tool against my anaconda python. I do this using sudo ./configure CXX="g++-5" CXXFLAGS="-std=gnu++14 -Wno-unused-local-typedefs" PYTHON="/home/pmj27/anaconda2/bin/python2.7" CAIROMM_LIBS="-L/home/pmj27/anaconda2/include/cairomm-1.0/cairomm" --enable-openmp (if I skip the sudo it won't pick up boost for reasons not quite known to me). I then run "sudo make -j20" followed by "make install". When opening python and importing the module I however get the error message Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/pmj27/anaconda2/lib/python2.7/site-packages/graph_tool/__init__.py", line 3323, in <module> openmp_set_schedule("static", 0) File "/home/pmj27/anaconda2/lib/python2.7/site-packages/graph_tool/__init__.py", line 3320, in openmp_set_schedule return libcore.openmp_set_schedule(schedule, chunk) Boost.Python.ArgumentError: Python argument types in graph_tool.libgraph_tool_core.openmp_set_schedule(str, int) did not match C++ signature: openmp_set_schedule(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int) My first thought was that graph-tool must be linking against an incorrect version of boost. So, following the advice from other posts, I ran ldd /home/pmj27/anaconda2/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so . This returns: linux-vdso.so.1 => (0x00007fffc93ce000) libpython2.7.so.1.0 => /home/pmj27/anaconda2/lib/libpython2.7.so.1.0 (0x00007fbcd05ec000) libboost_iostreams.so.1.63.0 => /home/pmj27/anaconda2/lib/libboost_iostreams.so.1.63.0 (0x00007fbcd03c4000) libboost_python.so.1.63.0 => /home/pmj27/anaconda2/lib/libboost_python.so.1.63.0 (0x00007fbcd0175000) libboost_regex.so.1.63.0 => /home/pmj27/anaconda2/lib/libboost_regex.so.1.63.0 (0x00007fbccfe5a000) libboost_coroutine.so.1.63.0 => /home/pmj27/anaconda2/lib/libboost_coroutine.so.1.63.0 (0x00007fbccfc50000) libexpat.so.1 => /home/pmj27/anaconda2/lib/libexpat.so.1 (0x00007fbccfa27000) libstdc++.so.6 => /home/pmj27/anaconda2/lib/libstdc++.so.6 (0x00007fbccf66b000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fbccf33c000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fbccef72000) libgcc_s.so.1 => /home/pmj27/anaconda2/lib/libgcc_s.so.1 (0x00007fbcced5b000) libgomp.so.1 => /home/pmj27/anaconda2/lib/libgomp.so.1 (0x00007fbcceb38000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fbcce91a000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fbcce716000) libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007fbcce513000) libz.so.1 => /home/pmj27/anaconda2/lib/./libz.so.1 (0x00007fbcce2fc000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fbcce0f4000) libicudata.so.56 => /home/pmj27/anaconda2/lib/./libicudata.so.56 (0x00007fbccc711000) libicui18n.so.56 => /home/pmj27/anaconda2/lib/./libicui18n.so.56 (0x00007fbccc214000) libicuuc.so.56 => /home/pmj27/anaconda2/lib/./libicuuc.so.56 (0x00007fbccbe2f000) libboost_context.so.1.63.0 => /home/pmj27/anaconda2/lib/./libboost_context.so.1.63.0 (0x00007fbccbc26000) libboost_thread.so.1.63.0 => /home/pmj27/anaconda2/lib/./libboost_thread.so.1.63.0 (0x00007fbccba04000) libboost_chrono.so.1.63.0 => /home/pmj27/anaconda2/lib/./libboost_chrono.so.1.63.0 (0x00007fbccb7fd000) libboost_system.so.1.63.0 => /home/pmj27/anaconda2/lib/./libboost_system.so.1.63.0 (0x00007fbccb5fa000) /lib64/ld-linux-x86-64.so.2 (0x000055cf9c8bc000) As far as I can tell all boost libraries are based on the anaconda boost libraries. Does anybody have any ideas what might be going wrong? Best, Philipp -- 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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Ordering vertex in NestedBlockState.draw()
by treinz 02 Mar '17

02 Mar '17

Hi all, I've been trying to order the vertices on the rim of a NSBM plot such that the labels, say, as integers, of two neighboring vertices are as close as possible. For example, if I have 5 vertices, I'd like them to be ordered 0-1-2-3-4 on the NSBM plot. Is there an easy way to do that? I know that this might have something to do with the 'pos' parameter but I didn't get the expected result after I play with it. Thanks, Tim

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