Re: [igraph] Re: igraph-help Digest, Vol 30, Issue 1

[Gábor Csárdi]

Please send me your file and tell me _exactly_ what you did. Please
tell me your R and igraph version too, the output of sessionInfo()
will do. The operating system version is useful too.

I cannot help you if I cannot reproduce your problem.

G.

ps. please choose a better subject line next time.
ps2. please consider subscribing to the mailing list, otherwise I will
have to acknowledge your messages by hand. (Or post from the address
you used to subscribe.)
ps3. please do _not_ include the whole digest in your email.

On Fri, Jan 2, 2009 at 12:34 AM, Aisan Kazerani
<address@hidden> wrote:
> Hi Gabor,
>
> Thanks for your advice, but there's still a RUNTIME error after I run my
> weighted betweenness program, saying:
>
> R FOR WINDOWS GUI FRONT-END HAS ENCOUNTERED A PROBLEM AND NEEDS TO CLOSE.
> WE ARE SORRY FOR THE ENCONVENIENCE.
>
> I have entered my graph manually using the graph command,not with pajek
> file this time. My graph has 57 vertices and 82 edges. Would you please
> help me out of this!!
>
> Thanks a lot..
> Aisan
>
>
>
>
>
>
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>> Today's Topics:
>>
>>    1. igraph 0.6 (Aisan Kazerani)
>>    2. igraph 0.6 (Aisan Kazerani)
>>    3. Re: igraph 0.6 ( G?bor Cs?rdi )
>>    4. Re: MCL Algorithm ( G?bor Cs?rdi )
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Thu, 01 Jan 2009 11:28:11 +1100 (EST)
>> From: Aisan Kazerani <address@hidden>
>> Subject: [igraph] igraph 0.6
>> To: address@hidden
>> Message-ID:
>>       <address@hidden>
>>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Dear sir,
>>
>> Does igraph package 0.6 work on Linux only, or does it work on windows as
>> well, because it doesn't consider the weights of edges for calculating
>> betweenness under R.
>>
>> Thanks.
>> Aisan Kazerani
>>
>>
>>
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 01 Jan 2009 12:11:47 +1100 (EST)
>> From: Aisan Kazerani <address@hidden>
>> Subject: [igraph] igraph 0.6
>> To: address@hidden
>> Message-ID:
>>       <address@hidden>
>>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Dear sir,
>>
>> Does igraph package 0.6 work on Linux only, or does it work on windows as
>> well, because it doesn't consider the weights of edges for calculating
>> betweenness under R in windows. My input is in pajek format with edge
>> weights, and these are my commands. But there is no difference between the
>> results of weighted betweenness and unweighted one.
>>
>> r <- read.graph ("test1.net", format="pajek")
>> betweenness(r)
>>
>> Thanks.
>> Aisan Kazerani
>>
>>
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Thu, 1 Jan 2009 10:42:55 +0100
>> From: " G?bor Cs?rdi " <address@hidden>
>> Subject: Re: [igraph] igraph 0.6
>> To: "Help for igraph users" <address@hidden>,         "Aisan
>>       Kazerani" <address@hidden>
>> Message-ID:
>>       <address@hidden>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> On Thu, Jan 1, 2009 at 2:11 AM, Aisan Kazerani
>> <address@hidden> wrote:
>>> Dear sir,
>>>
>>> Does igraph package 0.6 work on Linux only,
>>
>> No. Actually, if you have downloaded
>> http://cneurocvs.rmki.kfki.hu/igraph/download/igraph_0.6.zip
>> that is windows only.
>>
>>> or does it work on windows as
>>> well, because it doesn't consider the weights of edges for calculating
>>> betweenness under R in windows. My input is in pajek format with edge
>>> weights, and these are my commands. But there is no difference between
>>> the
>>> results of weighted betweenness and unweighted one.
>>>
>>> r <- read.graph ("test1.net", format="pajek")
>>> betweenness(r)
>>
>> Possible mistakes:
>> 1) your test1.net file does not have weights (check the file in an
>> editor),
>> 2) all weights in your file are the same (check the file in an editor),
>> 3) you are not using the 0.6 version of igraph (check the version you are
>> using,
>>     e.g. with library(help=igraph) )
>>
>> It definitely works for me (or gives different results in the weighted
>> case at least), both on Linux and Windows, I've just tried it:
>>
>>> library(igraph)
>>> g <- graph.ring(10)
>>> betweenness(g)
>>  [1] 8 8 8 8 8 8 8 8 8 8
>>> E(g)$weight <- runif(ecount(g))
>>> betweenness(g)
>>  [1]  4  6  8 10 12 12 11  9  7  5
>>
>> Best,
>> G.
>>
>>> Thanks.
>>> Aisan Kazerani
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> igraph-help mailing list
>>> address@hidden
>>> http://lists.nongnu.org/mailman/listinfo/igraph-help
>>>
>>
>>
>>
>> --
>> Gabor Csardi <address@hidden>     UNIL DGM
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Thu, 1 Jan 2009 11:14:12 +0100
>> From: " G?bor Cs?rdi " <address@hidden>
>> Subject: Re: [igraph] MCL Algorithm
>> To: "Help for igraph users" <address@hidden>
>> Message-ID:
>>       <address@hidden>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Thanks Chris, I've added your code to the (experimental and rather
>> empty) igraph wiki:
>> http://igraph.wikidot.com/community-detection-in-python
>> I hope you don't mind.
>>
>> G.
>>
>> On Wed, Dec 31, 2008 at 5:11 PM, Chris Wj <address@hidden> wrote:
>>> Well we certainly appreciate all the work you put in to the library.
>>>
>>> Quick Python code snippet I whipped up to test using MLC with igraph
>>> (uses
>>> subprocess and pipes):
>>>
>>> import igraph
>>>
>>> def igraph_to_mcl_matrix():
>>>     from subprocess import Popen, PIPE
>>>     from cStringIO import StringIO
>>>     G1 = igraph.Graph(n=3)
>>>     G1.add_edges(((0,1),(0,2),(1,2)))
>>>     mcifile = StringIO()
>>>     mclheader = (
>>>         ("\n(mclheader\n"),
>>>         ("mcltype matrix\n"),
>>>         ( "dimensions %sx%s\n)\n" % (G1.vcount(), G1.vcount()) ),
>>>         ("(mclmatrix\n"),
>>>         ("begin\n")
>>>     )
>>>     mcifile.writelines(mclheader)
>>>     for v in G1.vs:
>>>         mcifile.write(str(v.index) + " ")
>>>         for n in G1.neighbors(v.index):
>>>             mcifile.write(str(n) + " ")
>>>         mcifile.write(" $\n")
>>>     mcifile.write(")\n")
>>>     mcifile.seek(0)
>>>     cmd = "mcl - -o -"
>>>     p = Popen(cmd, stdout=PIPE, stdin=PIPE, stderr=PIPE)
>>>     sout,serr = p.communicate(mcifile.read())
>>>     p.wait()
>>>     #print "return code: %i\n" % p.returncode
>>>     if p.returncode==0 and len(sout)>0:
>>>         lines = sout.splitlines()
>>>         idx_begin = lines.index("begin")+1
>>>         idx_end = lines[idx_begin:].index(")")+idx_begin
>>>         for line in lines[idx_begin:idx_end]:
>>>             print line
>>>
>>> I used StringIO because I originally was using file IO before piping and
>>> it
>>> was easier to switch the code back and forth between string and file
>>> objects.
>>>
>>> On Wed, Dec 31, 2008 at 3:43 AM, G�bor Cs�rdi <address@hidden> wrote:
>>>>
>>>> Chris,
>>>>
>>>> this is always a difficult decision, the main problem is, that it is
>>>> not easy to do it in a way that allows us to include future updates as
>>>> well. Furthermore we will need to maintain the code in the future and
>>>> that is sometimes problematic, a large portion of portability problems
>>>> we get are due to some 3rd party C++ codes we put into igraph....
>>>>
>>>> We already include many smaller and bigger pieces of software, e.g.
>>>> the walktrap, the spinglass community finding algorithms, parts of
>>>> ARPACK, LAPACK and BLAS, the BLISS graph isomorphism library, etc.
>>>>
>>>> Maybe I am just frustrated because I have been trying to repair the
>>>> igraph version of ARPACK for a couple of days now....
>>>>
>>>> But actually the MCL code looks pretty good. So we will see. Thanks for
>>>> the tip.
>>>>
>>>> Best,
>>>> Gabor
>>>>
>>>> On Tue, Dec 30, 2008 at 11:20 PM, Chris Wj <address@hidden> wrote:
>>>> > I have been using MCL lately and before working on a way to export
>>>> > igraph in
>>>> > MCL matrix format, I was looking to see if there was any further
>>>> > thoughts on
>>>> > including this library in igraph. I searched the archives and found
>>>> that
>>>> > Tamas said something about possibly including MCL in igraph.
>>>> > For now, I will probably just exec it (popen) to test it.
>>>> >
>>>> > MCL: http://www.micans.org/mcl/
>>>> >
>>>> > _______________________________________________
>>>> > igraph-help mailing list
>>>> > address@hidden
>>>> > http://lists.nongnu.org/mailman/listinfo/igraph-help
>>>> >
>>>> >
>>>>
>>>>
>>>>
>>>> --
>>>> Gabor Csardi <address@hidden>     UNIL DGM
>>>>
>>>>
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>>>
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>>
>>
>>
>> --
>> Gabor Csardi <address@hidden>     UNIL DGM
>>
>>
>>
>>
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>> End of igraph-help Digest, Vol 30, Issue 1
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-- 
Gabor Csardi <address@hidden>     UNIL DGM