graph-tool November 2017

graph-tool@skewed.de

8 participants
15 discussions

get_out_degrees function issue
by Davide Baù 10 Nov '17

10 Nov '17

Hi, I'm trying to use the function "get_out_degrees", but I get following error: AttributeError: 'Graph' object has no attribute 'get_out_degrees' The graph I generated is a directed graph: <Graph object, directed, with 396 vertices and 10042 edges at 0x7fb5c15c5690> The gt version is the 2.18 (Ubuntu Trusty): '2.18 (commit 37996a0a, Thu Jul 21 17:56:14 2016 +0200)' Any idea of what I'm doing wrong? Thanks a lot! Davide

2 1

Error while updating
by Snehal Shekatkar 10 Nov '17

10 Nov '17

Dear Tiago, I am on Ubuntu 16.04 and while updating I got the following error. Err:16 http://downloads.skewed.de/apt/xenial xenial Release.gpg The following signatures were invalid: BADSIG 7A80C8ED4FCCBE09 Tiago de Paula Peixoto <tiago(a)skewed.de> So as per the instructions page, I tried: sudo apt-key adv --keyserver pgp.skewed.de --recv-key 612DEFB798507F25 However, this returns the following: Executing: /tmp/tmp.UgWxLPVkr2/gpg.1.sh --keyserver pgp.skewed.de --recv-key 612DEFB798507F25 gpg: requesting key 98507F25 from hkp server pgp.skewed.de gpgkeys: key 612DEFB798507F25 can't be retrieved gpg: no valid OpenPGP data found. gpg: Total number processed: 0 gpg: keyserver communications error: keyserver helper general error gpg: keyserver communications error: unknown pubkey algorithm gpg: keyserver receive failed: unknown pubkey algorithm What can be done? Thank you -- Snehal M. Shekatkar Pune India

2 1

Segmentation fault (core dumped) when running minimize_blockmodel_dl(g, overlap=True)
by Sanja Šćepanović 09 Nov '17

09 Nov '17

Hi All, I am experiencing the problem that I always get Segmentation fault (core dumped) and my program does not finish when running state = minimize_blockmodel_dl(g, overlap=True) When overlap=False, there is no problem. I have the 2.24 graph-tool version installed from Ubuntu repo. I tried this with both python2.7 and python3 -- in both cases, I get the segmentation fault error. Also, this is not due to the size of my graph, I tried with a toy example with only 10 nodes, it still happens. Any ideas what I could do are very much appreciated. Thanks, Sanja

4 6

Problems installing graph-tool with homebrew and python3 on macOS Sierra
by Kimon 06 Nov '17

06 Nov '17

Hey, I am getting the following errors: Kimons-MacBook-Pro:graph-tool-2.25 kimonfountoulakis$ brew instal -s --with-python3 graph-tool ==> Installing graph-tool from homebrew/science ==> Installing dependencies for homebrew/science/graph-tool: matplotlib, py2cairo, libcroco, librsvg, gnome-icon-theme, pygobject3 ==> Installing homebrew/science/graph-tool dependency: matplotlib ==> Downloading https://files.pythonhosted.org/packages/f5/f0/9da3ef24ea7eb0ccd12430a261b66… Already downloaded: /Users/kimonfountoulakis/Library/Caches/Homebrew/matplotlib-2.0.2.tar.gz ==> Downloading https://files.pythonhosted.org/packages/dc/8c/7c9869454bdc53e72fb87ace63eac… Already downloaded: /Users/kimonfountoulakis/Library/Caches/Homebrew/matplotlib--setuptools-33.1.1.zip ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/matplotlib/2.0.2/libexec --single-version-externally-managed --record=installed.txt ==> Downloading https://files.pythonhosted.org/packages/c2/4b/137dea450d6e1e3d474e1d873cd1d… Already downloaded: /Users/kimonfountoulakis/Library/Caches/Homebrew/matplotlib--Cycler-0.10.0.tar.gz ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/matplotlib/2.0.2/libexec --single-version-externally-managed --record=installed.txt ==> Downloading https://files.pythonhosted.org/packages/c5/60/6ac26ad05857c601308d8fb9e87fa… Already downloaded: /Users/kimonfountoulakis/Library/Caches/Homebrew/matplotlib--functools32-3.2.3-2.tar.gz ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/matplotlib/2.0.2/libexec --single-version-externally-managed --record=installed.txt ==> Downloading https://files.pythonhosted.org/packages/38/bb/bf325351dd8ab6eb3c3b7c07c3978… Already downloaded: /Users/kimonfountoulakis/Library/Caches/Homebrew/matplotlib--pyparsing-2.1.10.tar.gz ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/matplotlib/2.0.2/libexec --single-version-externally-managed --record=installed.txt ==> Downloading https://files.pythonhosted.org/packages/51/fc/39a3fbde6864942e8bb24c9366373… Already downloaded: /Users/kimonfountoulakis/Library/Caches/Homebrew/matplotlib--python-dateutil-2.6.0.tar.gz ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/matplotlib/2.0.2/libexec --single-version-externally-managed --record=installed.txt ==> Downloading https://files.pythonhosted.org/packages/d0/e1/aca6ef73a7bd322a7fc73fd99631e… Already downloaded: /Users/kimonfountoulakis/Library/Caches/Homebrew/matplotlib--pytz-2016.10.tar.bz2 ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/matplotlib/2.0.2/libexec --single-version-externally-managed --record=installed.txt ==> Downloading https://files.pythonhosted.org/packages/b3/b2/238e2590826bfdd113244a40d9d3e… Already downloaded: /Users/kimonfountoulakis/Library/Caches/Homebrew/matplotlib--six-1.10.0.tar.gz ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/matplotlib/2.0.2/libexec --single-version-externally-managed --record=installed.txt ==> Downloading https://files.pythonhosted.org/packages/b8/2f/49e53b0d0e94611a2dc624a1ad24d… Already downloaded: /Users/kimonfountoulakis/Library/Caches/Homebrew/matplotlib--subprocess32-3.2.7.tar.gz ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/matplotlib/2.0.2/libexec --single-version-externally-managed --record=installed.txt ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/matplotlib/2.0.2 --single-version-externally-managed --record=installed.txt Last 15 lines from /Users/kimonfountoulakis/Library/Logs/Homebrew/matplotlib/09.python: ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:322:9: error: no member named 'islessequal' in the global namespace using ::islessequal; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:323:9: error: no member named 'islessgreater' in the global namespace using ::islessgreater; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:324:9: error: no member named 'isunordered' in the global namespace using ::isunordered; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath:325:9: error: no member named 'isunordered' in the global namespace using ::isunordered; ~~^ 13 errors generated. error: command 'clang' failed with exit status 1 READ THIS: https://docs.brew.sh/Troubleshooting.html /usr/local/Homebrew/Library/Homebrew/utils/github.rb:210:in `raise_api_error': GitHub (GitHub::AuthenticationFailedError) The GitHub credentials in the macOS keychain may be invalid. Clear them with: printf "protocol=https\nhost=github.com\n" | git credential-osxkeychain erase Or create a personal access token: https://github.com/settings/tokens/new?scopes=gist,public_repo&description=… and then set the token as: export HOMEBREW_GITHUB_API_TOKEN="your_new_token" from /usr/local/Homebrew/Library/Homebrew/utils/github.rb:178:in `open' from /usr/local/Homebrew/Library/Homebrew/utils/github.rb:278:in `search' from /usr/local/Homebrew/Library/Homebrew/utils/github.rb:225:in `search_issues' from /usr/local/Homebrew/Library/Homebrew/utils/github.rb:238:in `issues_for_formula' from /usr/local/Homebrew/Library/Homebrew/exceptions.rb:369:in `fetch_issues' from /usr/local/Homebrew/Library/Homebrew/exceptions.rb:365:in `issues' from /usr/local/Homebrew/Library/Homebrew/exceptions.rb:419:in `dump' from /usr/local/Homebrew/Library/Homebrew/brew.rb:135:in `rescue in <main>' from /usr/local/Homebrew/Library/Homebrew/brew.rb:30:in `<main>' Any ideas? -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

3 14

disassortative constraints?
by Peter Straka 01 Nov '17

01 Nov '17

Hello, so clabel() and pclabel() serve as constraint labels: different values for nodes mean that nodes are placed in different groups, i.e. this is an assortative constraint (all nodes with the same label are place in one group). Is there a way to do a disassortative constraints: nodes with the same label are placed in different groups? Many thanks in advance, Peter -- Dr Peter Straka Senior Research Fellow (DECRA) in Statistics School of Mathematics & Statistics UNSW Sydney p.straka(a)unsw.edu.au | strakaps.github.io | @strakaps

2 1

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

graph-tool November 2017