October 2009 - graph-tool - archives.skewed.de

building graph-tool 2.0 under Mac OS X
by Claudio Martella 16 Oct '09

16 Oct '09

Hi, I'm trying to build graph-tool (from git) under my Mac OS X 10.4. I have installed through macports the libboost 1.40 (and boost::python support for python2.6). The configure script chooses to build for python 2.5, and therefore it cannot find boost::python Here's the configure output: checking for a Python interpreter with version >= 2.5... python checking for python... /opt/local/bin/python checking for python version... 2.6 checking for python platform... darwin checking for python script directory... ${prefix}/lib/python2.6/site-packages checking for python extension module directory... ${exec_prefix}/lib/python2.6/site-packages checking for python2.6... (cached) /opt/local/bin/python checking for a version of Python >= '2.1.0'... yes checking for a version of Python 2.5... yes checking for the distutils Python package... yes checking for Python include path... -I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 checking for Python library path... -L/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6 -lpython2.6 checking for Python site-packages path... /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages checking python extra libraries... -ldl checking python extra linking flags... -u _PyMac_Error /opt/local/Library/Frameworks/Python.framework/Versions/2.6/Python checking consistency of all components of python development environment... yes checking for boostlib >= 1.33.1... yes checking for python build information... checking for python2.5... python2.5 checking for main in -lpython2.5... yes checking python2.5/Python.h usability... yes checking python2.5/Python.h presence... yes checking for python2.5/Python.h... yes results of the Python check: Binary: python2.5 Library: python2.5 Include Dir: /Developer/SDKs/MacOSX10.5.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/include/python2.5 /System/Library/Frameworks/Python.framework/Versions/2.5/include/python2.5 checking whether the Boost::Python library is available... no configure: error: No usable boost::python found As you can see, python 2.6 is found at configure time, but it chooses to switch to 2.5 and i dunno why. i tried setting PYTHON_VERSION="2.6" but i still get the same problem. Do you have any suggestions about this problem? -- Claudio Martella claudio.martella(a)gmail.com

2 15

### LOVE LOVE VIAGRA LOVE LOVE ###
by VIAGRA � Official Site 14 Oct '09

14 Oct '09

Spam detection software, running on the system "forked.de", has identified this incoming email as possible spam. The original message has been attached to this so you can view it (if it isn't spam) or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: Professional LOVER Magazine: Web Exclusives Here's what's new... Welcome to the Professional LOVER E-Mail Newsletter, your preview of the latest product reviews, interviews and news you'll find only at Professional LOVER Online. [...] Content analysis details: (27.1 points, 5.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 3.5 BAYES_99 BODY: Bayesian spam probability is 99 to 100% [score: 1.0000] 0.0 MISSING_MID Missing Message-Id: header 0.0 MISSING_DATE Missing Date: header 2.0 RCVD_IN_BL_SPAMCOP_NET RBL: Received via a relay in bl.spamcop.net [Blocked - see <http://www.spamcop.net/bl.shtml?91.202.26.3>] 3.0 RCVD_IN_XBL RBL: Received via a relay in Spamhaus XBL [91.202.26.3 listed in zen.spamhaus.org] 0.6 RCVD_IN_SORBS_WEB RBL: SORBS: sender is a abuseable web server [91.202.26.3 listed in dnsbl.sorbs.net] 2.1 SUBJ_ALL_CAPS Subject is all capitals 2.0 URIBL_BLACK Contains an URL listed in the URIBL blacklist [URIs: rxlinguistics.cn] 1.9 URIBL_AB_SURBL Contains an URL listed in the AB SURBL blocklist [URIs: rxlinguistics.cn] 1.5 URIBL_WS_SURBL Contains an URL listed in the WS SURBL blocklist [URIs: rxlinguistics.cn] 1.5 URIBL_JP_SURBL Contains an URL listed in the JP SURBL blocklist [URIs: rxlinguistics.cn] 0.5 URIBL_SC_SURBL Contains an URL listed in the SC SURBL blocklist [URIs: rxlinguistics.cn] 0.3 DRUG_ED_CAPS BODY: Mentions an E.D. drug 1.6 HTML_IMAGE_ONLY_28 BODY: HTML: images with 2400-2800 bytes of words 0.0 HTML_MESSAGE BODY: HTML included in message 1.5 MIME_HTML_ONLY BODY: Message only has text/html MIME parts 1.5 RAZOR2_CF_RANGE_E8_51_100 Razor2 gives engine 8 confidence level above 50% [cf: 100] 1.5 RAZOR2_CF_RANGE_E4_51_100 Razor2 gives engine 4 confidence level above 50% [cf: 100] 0.5 RAZOR2_CHECK Listed in Razor2 (http://razor.sf.net/) 0.5 RAZOR2_CF_RANGE_51_100 Razor2 gives confidence level above 50% [cf: 100] 2.2 DCC_CHECK Listed in DCC (http://rhyolite.com/anti-spam/dcc/) 1.5 URIBL_SBL Contains an URL listed in the SBL blocklist [URIs: rxlinguistics.cn] 0.0 DIGEST_MULTIPLE Message hits more than one network digest check 0.3 DRUGS_ERECTILE Refers to an erectile drug 0.1 RDNS_NONE Delivered to trusted network by a host with no rDNS -2.8 AWL AWL: From: address is in the auto white-list The original message was not completely plain text, and may be unsafe to open with some email clients; in particular, it may contain a virus, or confirm that your address can receive spam. If you wish to view it, it may be safer to save it to a file and open it with an editor.

1 0

ubuntu packages compiled for parallel computation
by Claudio Martella 09 Oct '09

09 Oct '09

Hi, just wanted to ask if the prebuilt packages for ubuntu are compiled for parallel computation with openMP. thanks -- Claudio Martella claudio.martella(a)gmail.com

2 1

Error in drawing graphs
by Karthik Channakeshava 09 Oct '09

09 Oct '09

Hi, I am trying the example code for drawing the graphs on my machine. Here is the error I am getting. I am sure this is something to do with the installed packages. I am using Debian and am not sure what package or path is missing. ****** Traceback (most recent call last): File "gt_draw_graph.py", line 23, in <module> penwidth=ebet, overlap="prism", output="graph-draw.png") File "/usr/local/lib/python2.5/site-packages/graph_tool/draw/__init__.py", line 264, in graph_draw gvg = gv.graph("G") NameError: global name 'gv' is not defined ****** TIA, Karthik

3 2

Vertex label reordering
by Juan Manuel Tirado 09 Oct '09

09 Oct '09

Hi everyone, I've been working around with graph-tool and I have found a strange behaviour. A have this input .dot file graph G { 0 ; 10 ; 200 ; 1000 ; 0--200 ; 10--200 ; 1000--200 ; 1000--10 ; } I load the graph in graph_tool using g=load_graph("example.dot") and everything is OK. Now I want to know the output_degree of the node with identifier 200 (index 2). I use: g.vertex(2).out_degree() that returns 2 Obviously vertex with identifier 200 (index 2) must return 3. I have executed g.save("graphtool_dump.dot") with the following output: graph G { 0; 10; 1000; 200; 0--200 ; 10--200 ; 1000--200 ; 1000--10 ; } The nodes have been reordered (probably following alphabetic order) and now the vertex with identifier "200" is in position 3 instead of 2. This behaviour can be very annoying in some cases, and can lead to confusion. Does exist any way to avoid this reordering? Thanks in advance, Juan

2 1

local_clustering returned array
by Juan Manuel Tirado 07 Oct '09

07 Oct '09

I have the following code g=load_graph("graph.xml") clust=local_clustering(g) for i in clust.get_array(): print i This code returns something like 0.0 0.333333 1.5 ....etc What I would like to do is to print the vertex identifier that corresponds to every clustering coefficient. The output to get is something like: edge1 0.0 edge2 0.33333 edge3 1.5 .....etc. I suppose that this is really simple, but I'm newbie at python I do not get how to do it. I appreciate your help and comments. Juan

2 2

[announcement] New version from graph-tool
by Tiago de Paula Peixoto 07 Oct '09

07 Oct '09

I'm happy to announce version 2.0.0 from graph-tool! What is new? ============ Python module ------------- It is the first stable release since years ago, and marks a full transition of graph-tool from a stand-alone program to a full python module. It is pointless to summarize all the differences, since everything changed. The new version is, for me, a lot more comfortable to work with, and the internals are a lot cleaner. Everything integrates nicely with scipy/numpy, and I hope graph-tool will be a nice addition to this framework. More algorithms ---------------- The number of algorithms has increased significantly. Now there is support for maximum flow, pagerank, motifs, isomorphism, and many more. Most algorithms in the Boost Graph Library are now available in graph-tool. Documentation ------------- This version includes full documentation, with code examples, available online and from the docstrings. The documentation has 100% coverage of every function and data structure. Read it in all its glory at: https://projects.forked.de/graph-tool/doc/ Bug fixes ========= Several. Just dig into the git archive to see the gory details: http://git.forked.de/?p=graph-tool Where to get ============ Get it from the usual place: https://projects.forked.de/graph-tool/wiki/GraphToolDownload Packages! --------- Pre-build packages are also available for Debian and Ubuntu, for those who don't want (or can't) compile everything from source. Best regards, and enjoy! Tiago

3 5