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The Basics
Id: 19480
Status: resolved
Priority: 0/
Queue: Graph
People
Owner: Nobody in particular
Requestors: osborne1 [...] optonline.net
Cc:
AdminCc:
Bug Information
Severity: Important
Broken in: 0.71
Fixed in: 0.69
Attachments
Graph-0.72.tar.gz
Graph-MD5.t
network1.txt
node-list.txt

History Show all quoted text
  Thu May 25 12:17:56 2006 Guest - Ticket created
Subject: articulation_points stalls
Jarrko, It's great that you've been able to work on those bugs relating to refvertexed. I haven't been able to fully test the fixes yet but I will get around to examing them shortly. Meanwhile I've encountered a problem with articulation_points that I hadn't seen using .69. The problem is that the script stalls at this method and never finishes. I've reduced the problem down to a plain network so that you don't need to install BioPerl to see it. Details: Mac OS X 10.4.6, perl 5.8.6. Graph .71 Code: #!/usr/bin/perl -w use strict; use Graph; my $g = Graph::Undirected->new; open MYIN,"network1.txt"; while (<MYIN>) { chomp; my ($e,$v1,$v2) = split ','; $g->add_vertices($v1,$v2); $g->add_edges([$v1,$v2]); } my @rts = $g->articulation_points; print "@rts\n"; Thanks again, BIO Than
Subject: network1.txt
DIP:4305E,DIP:3048N,DIP:3047N DIP:4307E,DIP:3050N,DIP:3047N DIP:4308E,DIP:3051N,DIP:3051N DIP:4309E,DIP:3052N,DIP:3051N DIP:4310E,DIP:3053N,DIP:3051N DIP:4311E,DIP:3054N,DIP:3051N DIP:4312E,DIP:3055N,DIP:3056N DIP:4313E,DIP:3057N,DIP:3056N DIP:4314E,DIP:3058N,DIP:3056N DIP:4315E,DIP:3059N,DIP:3056N DIP:4316E,DIP:3060N,DIP:3056N DIP:4317E,DIP:3061N,DIP:3056N DIP:4318E,DIP:3062N,DIP:3056N DIP:4319E,DIP:3063N,DIP:3056N DIP:4320E,DIP:3064N,DIP:3056N DIP:4321E,DIP:3065N,DIP:3056N DIP:4322E,DIP:3066N,DIP:3056N DIP:4323E,DIP:3067N,DIP:3056N DIP:4324E,DIP:3053N,DIP:3056N DIP:4325E,DIP:3068N,DIP:3056N DIP:4326E,DIP:3070N,DIP:3069N DIP:4327E,DIP:3071N,DIP:3069N DIP:4328E,DIP:3072N,DIP:3069N DIP:4329E,DIP:3073N,DIP:3069N DIP:4330E,DIP:3074N,DIP:3074N DIP:4331E,DIP:3053N,DIP:3074N DIP:4332E,DIP:3075N,DIP:3075N DIP:4333E,DIP:3076N,DIP:3075N DIP:4334E,DIP:3077N,DIP:3075N DIP:4335E,DIP:3078N,DIP:3075N DIP:4336E,DIP:3079N,DIP:3075N DIP:4337E,DIP:3080N,DIP:3075N DIP:4338E,DIP:3081N,DIP:3075N DIP:4339E,DIP:3082N,DIP:3075N DIP:4340E,DIP:3083N,DIP:3075N DIP:4341E,DIP:3084N,DIP:3075N DIP:4342E,DIP:3085N,DIP:3075N DIP:4343E,DIP:3086N,DIP:3075N DIP:4344E,DIP:3087N,DIP:3075N DIP:4345E,DIP:3088N,DIP:3075N DIP:4346E,DIP:3090N,DIP:3089N DIP:4347E,DIP:3091N,DIP:3089N DIP:4348E,DIP:3092N,DIP:3089N DIP:4349E,DIP:3093N,DIP:3089N DIP:4350E,DIP:3094N,DIP:3089N DIP:4351E,DIP:3082N,DIP:3089N DIP:4352E,DIP:3083N,DIP:3089N DIP:4353E,DIP:3095N,DIP:3089N DIP:4354E,DIP:3096N,DIP:3089N DIP:4355E,DIP:3097N,DIP:3089N DIP:4356E,DIP:3087N,DIP:3089N DIP:4357E,DIP:3098N,DIP:3089N DIP:4358E,DIP:3099N,DIP:3089N DIP:4359E,DIP:3100N,DIP:3089N DIP:4360E,DIP:3102N,DIP:3101N DIP:4361E,DIP:3103N,DIP:3101N DIP:4362E,DIP:3104N,DIP:3101N DIP:4363E,DIP:3095N,DIP:3101N DIP:4364E,DIP:3105N,DIP:3101N DIP:4365E,DIP:3106N,DIP:3101N DIP:4366E,DIP:3107N,DIP:3107N DIP:4367E,DIP:3108N,DIP:3108N DIP:4368E,DIP:3110N,DIP:3109N DIP:4369E,DIP:3111N,DIP:3109N DIP:4370E,DIP:3112N,DIP:3109N DIP:4384E,DIP:3112N,DIP:3111N DIP:4371E,DIP:3059N,DIP:3109N DIP:4372E,DIP:3113N,DIP:3109N DIP:4373E,DIP:3114N,DIP:3109N DIP:4374E,DIP:3115N,DIP:3109N DIP:4375E,DIP:3116N,DIP:3109N DIP:4376E,DIP:3117N,DIP:3109N DIP:4377E,DIP:3118N,DIP:3109N DIP:4378E,DIP:3119N,DIP:3119N DIP:4379E,DIP:3053N,DIP:3119N DIP:4380E,DIP:3120N,DIP:3120N DIP:4381E,DIP:3121N,DIP:3120N DIP:4382E,DIP:3122N,DIP:3120N DIP:4383E,DIP:3103N,DIP:3123N DIP:4389E,DIP:3103N,DIP:3123N DIP:4390E,DIP:3103N,DIP:3123N DIP:4391E,DIP:3122N,DIP:3120N DIP:4391E,DIP:3122N,DIP:3120N
  Thu May 25 14:15:05 2006 jhi [...] iki.fi - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Thu, 25 May 2006 21:14:28 +0300
To: bug-Graph [...] rt.cpan.org
From: Jarkko Hietaniemi <jhietaniemi [...] gmail.com>
Guest via RT wrote: Show quoted text
> Thu May 25 12:17:56 2006: Request 19480 was acted upon. > Transaction: Ticket created by guest > Queue: Graph > Subject: articulation_points stalls > Broken in: 0.71 > Severity: Important > Owner: Nobody > Requestors: osborne1@optonline.net > Status: new > Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > > > > Jarrko, > > It's great that you've been able to work on those bugs relating to refvertexed. I haven't been > able to fully test the fixes yet but I will get around to examing them shortly. Meanwhile I've > encountered a problem with articulation_points that I hadn't seen using .69. The problem is > that the script stalls at this method and never finishes. I've reduced the problem down to a > plain network so that you don't need to install BioPerl to see it. Details: > > Mac OS X 10.4.6, perl 5.8.6. Graph .71
Is DIP:3053N DIP:3089N DIP:3075N DIP:3056N DIP:3109N DIP:3069N DIP:3120N DIP:3047N DIP:3103N DIP:3051N DIP:3101N DIP:3059N DIP:3095N the correct answer? Show quoted text
> Code: > > #!/usr/bin/perl -w > > use strict; > use Graph; > > my $g = Graph::Undirected->new; > > open MYIN,"network1.txt"; > > while (<MYIN>) { > chomp; > my ($e,$v1,$v2) = split ','; > $g->add_vertices($v1,$v2); > $g->add_edges([$v1,$v2]); > } > > my @rts = $g->articulation_points; > > print "@rts\n"; > > > > Thanks again, > > BIO > > Than
  Thu May 25 14:15:05 2006 The RT System itself - Status changed from 'new' to 'open'
  Thu May 25 15:39:46 2006 osborne1 [...] optonline.net - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Thu, 25 May 2006 15:39:11 -0400
To: bug-Graph [...] rt.cpan.org
From: Brian Osborne <osborne1 [...] optonline.net>
Jarrko, I don't know, strange as this may sound. However, if you commit your fix then I will check the results from articulation_points using some other networks to verify. My network viewer cannot import plain text files but I have access to unlimited numbers of networks in various XML formats. BIO On 5/25/06 2:15 PM, "jhi@iki.fi via RT" <bug-Graph@rt.cpan.org> wrote: Show quoted text
> > <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > > > Guest via RT wrote:
>> Thu May 25 12:17:56 2006: Request 19480 was acted upon. >> Transaction: Ticket created by guest >> Queue: Graph >> Subject: articulation_points stalls >> Broken in: 0.71 >> Severity: Important >> Owner: Nobody >> Requestors: osborne1@optonline.net >> Status: new >> Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > >> >> >> Jarrko, >> >> It's great that you've been able to work on those bugs relating to >> refvertexed. I haven't been >> able to fully test the fixes yet but I will get around to examing them >> shortly. Meanwhile I've >> encountered a problem with articulation_points that I hadn't seen using .69. >> The problem is >> that the script stalls at this method and never finishes. I've reduced the >> problem down to a >> plain network so that you don't need to install BioPerl to see it. Details: >> >> Mac OS X 10.4.6, perl 5.8.6. Graph .71
> > Is > > DIP:3053N DIP:3089N DIP:3075N DIP:3056N DIP:3109N DIP:3069N DIP:3120N > DIP:3047N DIP:3103N DIP:3051N DIP:3101N DIP:3059N DIP:3095N > > the correct answer? >
>> Code: >> >> #!/usr/bin/perl -w >> >> use strict; >> use Graph; >> >> my $g = Graph::Undirected->new; >> >> open MYIN,"network1.txt"; >> >> while (<MYIN>) { >> chomp; >> my ($e,$v1,$v2) = split ','; >> $g->add_vertices($v1,$v2); >> $g->add_edges([$v1,$v2]); >> } >> >> my @rts = $g->articulation_points; >> >> print "@rts\n"; >> >> >> >> Thanks again, >> >> BIO >> >> Than
> >
  Thu May 25 15:48:04 2006 jhi [...] iki.fi - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Thu, 25 May 2006 22:46:23 +0300
To: bug-Graph [...] rt.cpan.org
From: Jarkko Hietaniemi <jhietaniemi [...] gmail.com>
osborne1@optonline.net via RT wrote: Show quoted text
> Queue: Graph > Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > > > Jarrko, > > I don't know, strange as this may sound. However, if you commit your fix > then I will check the results from articulation_points using some other > networks to verify. My network viewer cannot import plain text files but I > have access to unlimited numbers of networks in various XML formats.
Okay, try the attached one. It is NOT yet the real 0.72. Show quoted text
> BIO > > > On 5/25/06 2:15 PM, "jhi@iki.fi via RT" <bug-Graph@rt.cpan.org> wrote: >
>> <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > >> >> Guest via RT wrote:
>>> Thu May 25 12:17:56 2006: Request 19480 was acted upon. >>> Transaction: Ticket created by guest >>> Queue: Graph >>> Subject: articulation_points stalls >>> Broken in: 0.71 >>> Severity: Important >>> Owner: Nobody >>> Requestors: osborne1@optonline.net >>> Status: new >>> Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > >>> >>> >>> Jarrko, >>> >>> It's great that you've been able to work on those bugs relating to >>> refvertexed. I haven't been >>> able to fully test the fixes yet but I will get around to examing them >>> shortly. Meanwhile I've >>> encountered a problem with articulation_points that I hadn't seen using .69. >>> The problem is >>> that the script stalls at this method and never finishes. I've reduced the >>> problem down to a >>> plain network so that you don't need to install BioPerl to see it. Details: >>> >>> Mac OS X 10.4.6, perl 5.8.6. Graph .71
>> Is >> >> DIP:3053N DIP:3089N DIP:3075N DIP:3056N DIP:3109N DIP:3069N DIP:3120N >> DIP:3047N DIP:3103N DIP:3051N DIP:3101N DIP:3059N DIP:3095N >> >> the correct answer? >>
>>> Code: >>> >>> #!/usr/bin/perl -w >>> >>> use strict; >>> use Graph; >>> >>> my $g = Graph::Undirected->new; >>> >>> open MYIN,"network1.txt"; >>> >>> while (<MYIN>) { >>> chomp; >>> my ($e,$v1,$v2) = split ','; >>> $g->add_vertices($v1,$v2); >>> $g->add_edges([$v1,$v2]); >>> } >>> >>> my @rts = $g->articulation_points; >>> >>> print "@rts\n"; >>> >>> >>> >>> Thanks again, >>> >>> BIO >>> >>> Than
>>
> > > >
Download Graph-0.72.tar.gz
application/x-gzip 97.4k

Message body not shown because it is not plain text.

  Fri May 26 17:35:24 2006 osborne1 [...] optonline.net - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Fri, 26 May 2006 17:34:50 -0400
To: bug-Graph [...] rt.cpan.org
From: Brian Osborne <osborne1 [...] optonline.net>
Jarrko, I've tested this pre-.72 with 5 different networks and articulation_points() is performing correctly on them. One of these was reasonably complex, it's likely that this method is working. BIO On 5/25/06 3:48 PM, "jhi@iki.fi via RT" <bug-Graph@rt.cpan.org> wrote: Show quoted text
> > <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > > > osborne1@optonline.net via RT wrote:
>> Queue: Graph >> Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > >> >> Jarrko, >> >> I don't know, strange as this may sound. However, if you commit your fix >> then I will check the results from articulation_points using some other >> networks to verify. My network viewer cannot import plain text files but I >> have access to unlimited numbers of networks in various XML formats.
> > Okay, try the attached one. It is NOT yet the real 0.72. >
>> BIO >> >> >> On 5/25/06 2:15 PM, "jhi@iki.fi via RT" <bug-Graph@rt.cpan.org> wrote: >>
>>> <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > >>> >>> Guest via RT wrote:
>>>> Thu May 25 12:17:56 2006: Request 19480 was acted upon. >>>> Transaction: Ticket created by guest >>>> Queue: Graph >>>> Subject: articulation_points stalls >>>> Broken in: 0.71 >>>> Severity: Important >>>> Owner: Nobody >>>> Requestors: osborne1@optonline.net >>>> Status: new >>>> Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > >>>> >>>> >>>> Jarrko, >>>> >>>> It's great that you've been able to work on those bugs relating to >>>> refvertexed. I haven't been >>>> able to fully test the fixes yet but I will get around to examing them >>>> shortly. Meanwhile I've >>>> encountered a problem with articulation_points that I hadn't seen using >>>> .69. >>>> The problem is >>>> that the script stalls at this method and never finishes. I've reduced the >>>> problem down to a >>>> plain network so that you don't need to install BioPerl to see it. Details: >>>> >>>> Mac OS X 10.4.6, perl 5.8.6. Graph .71
>>> Is >>> >>> DIP:3053N DIP:3089N DIP:3075N DIP:3056N DIP:3109N DIP:3069N DIP:3120N >>> DIP:3047N DIP:3103N DIP:3051N DIP:3101N DIP:3059N DIP:3095N >>> >>> the correct answer? >>>
>>>> Code: >>>> >>>> #!/usr/bin/perl -w >>>> >>>> use strict; >>>> use Graph; >>>> >>>> my $g = Graph::Undirected->new; >>>> >>>> open MYIN,"network1.txt"; >>>> >>>> while (<MYIN>) { >>>> chomp; >>>> my ($e,$v1,$v2) = split ','; >>>> $g->add_vertices($v1,$v2); >>>> $g->add_edges([$v1,$v2]); >>>> } >>>> >>>> my @rts = $g->articulation_points; >>>> >>>> print "@rts\n"; >>>> >>>> >>>> >>>> Thanks again, >>>> >>>> BIO >>>> >>>> Than
>>>
>> >> >> >>
> >
  Fri May 26 17:46:34 2006 jhi [...] iki.fi - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Sat, 27 May 2006 00:45:29 +0300
To: bug-Graph [...] rt.cpan.org
From: Jarkko Hietaniemi <jhietaniemi [...] gmail.com>
osborne1@optonline.net via RT wrote: Show quoted text
> Queue: Graph > Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > > > Jarrko, > > I've tested this pre-.72 with 5 different networks and articulation_points() > is performing correctly on them. One of these was reasonably complex, it's > likely that this method is working. > > BIO
Great, thanks for testing! Can some (smaller) ones (one or two) of these networks be "donated" to Graph as test cases?
  Fri May 26 18:01:42 2006 jhi [...] iki.fi - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Sat, 27 May 2006 00:56:06 +0300
To: bug-Graph [...] rt.cpan.org
From: Jarkko Hietaniemi <jhietaniemi [...] gmail.com>
Jarkko Hietaniemi wrote: Show quoted text
> osborne1@optonline.net via RT wrote:
>> Queue: Graph >> Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > >> >> Jarrko, >> >> I've tested this pre-.72 with 5 different networks and articulation_points() >> is performing correctly on them. One of these was reasonably complex, it's >> likely that this method is working. >> >> BIO
> > Great, thanks for testing! Can some (smaller) ones (one or two) of > these networks be "donated" to Graph as test cases?
The one that stalled would be a great test... (it stalled because of self-loops.) Show quoted text
> >
  Fri May 26 18:15:27 2006 osborne1 [...] optonline.net - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Fri, 26 May 2006 18:05:36 -0400
To: bug-Graph [...] rt.cpan.org
From: Brian Osborne <osborne1 [...] optonline.net>
Jarrko, Yes, feel free to use that, no problem. BIO On 5/26/06 6:01 PM, "jhi@iki.fi via RT" <bug-Graph@rt.cpan.org> wrote: Show quoted text
> > <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > > > Jarkko Hietaniemi wrote:
>> osborne1@optonline.net via RT wrote:
>>> Queue: Graph >>> Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > >>> >>> Jarrko, >>> >>> I've tested this pre-.72 with 5 different networks and articulation_points() >>> is performing correctly on them. One of these was reasonably complex, it's >>> likely that this method is working. >>> >>> BIO
>> >> Great, thanks for testing! Can some (smaller) ones (one or two) of >> these networks be "donated" to Graph as test cases?
> > The one that stalled would be a great test... (it stalled because > of self-loops.) >
>> >>
> >
  Sat May 27 02:08:32 2006 jhi [...] iki.fi - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Sat, 27 May 2006 09:07:27 +0300
To: bug-Graph [...] rt.cpan.org
From: Jarkko Hietaniemi <jhietaniemi [...] gmail.com>
Graph 0.72 uploaded to CPAN, thanks for your help!
  Sat May 27 11:36:42 2006 JHI [...] cpan.org - Correspondence added
Graph 0.72 should have this fixed.
  Sat May 27 11:36:43 2006 JHI [...] cpan.org - Status changed from 'open' to 'resolved'
  Sat May 27 15:17:57 2006 jhi [...] iki.fi - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Sat, 27 May 2006 22:17:29 +0300
To: bug-Graph [...] rt.cpan.org
From: Jarkko Hietaniemi <jhietaniemi [...] gmail.com>
Somewhat bad news: there is still something wrong, articulation_points() seems to randomly return nothing (no points). Somewhat good news: I'm on it.
  Sat May 27 15:17:58 2006 The RT System itself - Status changed from 'resolved' to 'open'
  Sat May 27 16:32:47 2006 jhi [...] iki.fi - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Sat, 27 May 2006 23:32:00 +0300
To: bug-Graph [...] rt.cpan.org
From: Jarkko Hietaniemi <jhietaniemi [...] gmail.com>
0.73...
  Sat May 27 16:57:35 2006 osborne1 [...] optonline.net - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Sat, 27 May 2006 16:56:22 -0400
To: bug-Graph [...] rt.cpan.org
From: Brian Osborne <osborne1 [...] optonline.net>
Jarrko, No problem. In a day or two I'll send you another "plain" network/graph, this is one whose articulation points have been independently verified but unfortunately I've hit some bugs of my own! BIO On 5/27/06 2:08 AM, "jhi@iki.fi via RT" <bug-Graph@rt.cpan.org> wrote: Show quoted text
> > <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > > > Graph 0.72 uploaded to CPAN, thanks for your help! > >
  Sat May 27 17:00:23 2006 osborne1 [...] optonline.net - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Sat, 27 May 2006 16:58:58 -0400
To: bug-Graph [...] rt.cpan.org
From: Brian Osborne <osborne1 [...] optonline.net>
Jarrko, Actually I'm kind of glad of you're seeing problems, I'm still having trouble with refvertex'ing and articulation_points but it's intermittent, sometimes I see it, sometimes I don't. BIO On 5/27/06 3:17 PM, "jhi@iki.fi via RT" <bug-Graph@rt.cpan.org> wrote: Show quoted text
> > <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > > > Somewhat bad news: there is still something wrong, > articulation_points() seems to randomly return nothing > (no points). Somewhat good news: I'm on it. > > >
  Sat May 27 17:44:22 2006 jhi [...] iki.fi - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Sun, 28 May 2006 00:44:06 +0300
To: bug-Graph [...] rt.cpan.org
From: Jarkko Hietaniemi <jhietaniemi [...] gmail.com>
osborne1@optonline.net via RT wrote: Show quoted text
> Queue: Graph > Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > > > Jarrko, > > Actually I'm kind of glad of you're seeing problems, I'm still having > trouble with refvertex'ing and articulation_points but it's intermittent, > sometimes I see it, sometimes I don't.
articulation_points() should now be better in Graph 0.73, if you get any details (like a test case failure) for the refvertexing, that would be great. Show quoted text
> BIO > > > On 5/27/06 3:17 PM, "jhi@iki.fi via RT" <bug-Graph@rt.cpan.org> wrote: >
>> <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > >> >> Somewhat bad news: there is still something wrong, >> articulation_points() seems to randomly return nothing >> (no points). Somewhat good news: I'm on it. >> >> >>
> > > >
  Tue May 30 10:14:06 2006 osborne1 [...] optonline.net - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Tue, 30 May 2006 10:13:14 -0400
To: bug-Graph [...] rt.cpan.org
From: Brian Osborne <osborne1 [...] optonline.net>
Jarrko, Here's a test for articulation_points that I've verified, the 8 nodes that should be returned by the method are: EBI-621930 EBI-622235 EBI-622306 EBI-622281 EBI-622264 EBI-622203 EBI-622140 EBI-622382 Code is something like: use strict; use Graph; my $g = Graph::Undirected->new; open MYIN,"node-list.txt"; while (<MYIN>) { chomp; my ($v1,$v2) = split ' '; $g->add_vertices($v1,$v2); $g->add_edges([$v1,$v2]); } The input file is attached. BIO my @rts = $g->articulation_points; On 5/27/06 5:44 PM, "jhi@iki.fi via RT" <bug-Graph@rt.cpan.org> wrote: Show quoted text
> > <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > > > osborne1@optonline.net via RT wrote:
>> Queue: Graph >> Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > >> >> Jarrko, >> >> Actually I'm kind of glad of you're seeing problems, I'm still having >> trouble with refvertex'ing and articulation_points but it's intermittent, >> sometimes I see it, sometimes I don't.
> > articulation_points() should now be better in Graph 0.73, > if you get any details (like a test case failure) for the > refvertexing, that would be great. >
>> BIO >> >> >> On 5/27/06 3:17 PM, "jhi@iki.fi via RT" <bug-Graph@rt.cpan.org> wrote: >>
>>> <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > >>> >>> Somewhat bad news: there is still something wrong, >>> articulation_points() seems to randomly return nothing >>> (no points). Somewhat good news: I'm on it. >>> >>> >>>
>> >> >> >>
> >
Download node-list.txt
application/octet-stream 5.5k

Message body not shown because it is not plain text.

  Tue May 30 11:36:51 2006 osborne1 [...] optonline.net - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Tue, 30 May 2006 11:35:09 -0400
To: bug-Graph [...] rt.cpan.org
From: Brian Osborne <osborne1 [...] optonline.net>
Jarrko, I'm attaching a *t file that has some of my tests on refvertexing. Most methods tested work, but a couple of methods don't (and I'm not sure if my usage of connected_graph() is correct). BIO On 5/27/06 5:44 PM, "jhi@iki.fi via RT" <bug-Graph@rt.cpan.org> wrote: Show quoted text
> > <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > > > osborne1@optonline.net via RT wrote:
>> Queue: Graph >> Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > >> >> Jarrko, >> >> Actually I'm kind of glad of you're seeing problems, I'm still having >> trouble with refvertex'ing and articulation_points but it's intermittent, >> sometimes I see it, sometimes I don't.
> > articulation_points() should now be better in Graph 0.73, > if you get any details (like a test case failure) for the > refvertexing, that would be great. >
>> BIO >> >> >> On 5/27/06 3:17 PM, "jhi@iki.fi via RT" <bug-Graph@rt.cpan.org> wrote: >>
>>> <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > >>> >>> Somewhat bad news: there is still something wrong, >>> articulation_points() seems to randomly return nothing >>> (no points). Somewhat good news: I'm on it. >>> >>> >>>
>> >> >> >>
> >

Message body is not shown because sender requested not to inline it.

  Tue May 30 12:44:46 2006 jhi [...] iki.fi - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Tue, 30 May 2006 19:43:59 +0300
To: bug-Graph [...] rt.cpan.org
From: Jarkko Hietaniemi <jhietaniemi [...] gmail.com>
osborne1@optonline.net via RT wrote: Show quoted text
> Queue: Graph > Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > > > Jarrko, > > Here's a test for articulation_points that I've verified, the 8 nodes that > should be returned by the method are: > > EBI-621930 EBI-622235 EBI-622306 EBI-622281 EBI-622264 EBI-622203 EBI-622140 > EBI-622382 > > Code is something like: > > use strict; > use Graph; > > my $g = Graph::Undirected->new; > > open MYIN,"node-list.txt"; > > while (<MYIN>) { > chomp; > my ($v1,$v2) = split ' '; > $g->add_vertices($v1,$v2); > $g->add_edges([$v1,$v2]); > }
Thanks. By the way, you do not need to add_vertices(), the add_edges() will do it for you automatically.
  Tue May 30 13:01:24 2006 osborne1 [...] optonline.net - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Tue, 30 May 2006 13:00:39 -0400
To: bug-Graph [...] rt.cpan.org
From: Brian Osborne <osborne1 [...] optonline.net>
Got it. On 5/30/06 12:44 PM, "jhi@iki.fi via RT" <bug-Graph@rt.cpan.org> wrote: Show quoted text
> > <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > > > osborne1@optonline.net via RT wrote:
>> Queue: Graph >> Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > >> >> Jarrko, >> >> Here's a test for articulation_points that I've verified, the 8 nodes that >> should be returned by the method are: >> >> EBI-621930 EBI-622235 EBI-622306 EBI-622281 EBI-622264 EBI-622203 EBI-622140 >> EBI-622382 >> >> Code is something like: >> >> use strict; >> use Graph; >> >> my $g = Graph::Undirected->new; >> >> open MYIN,"node-list.txt"; >> >> while (<MYIN>) { >> chomp; >> my ($v1,$v2) = split ' '; >> $g->add_vertices($v1,$v2); >> $g->add_edges([$v1,$v2]); >> }
> > Thanks. By the way, you do not need to add_vertices(), the add_edges() > will do it for you automatically. > >
  Tue May 30 13:12:07 2006 jhi [...] iki.fi - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Tue, 30 May 2006 20:11:46 +0300
To: bug-Graph [...] rt.cpan.org
From: Jarkko Hietaniemi <jhietaniemi [...] gmail.com>
osborne1@optonline.net via RT wrote: Show quoted text
> Queue: Graph > Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > > > Jarrko, > > I'm attaching a *t file that has some of my tests on refvertexing. Most
Thanks! Do you mind if I "borrow" these sets? Show quoted text
> methods tested work, but a couple of methods don't (and I'm not sure if my > usage of connected_graph() is correct).
No, it's not. The "supercomponents" of connected graphs do not by default belong to any useful package, i.e. they are not usable Perl objects. This is because there is no way for Perl to know how you want your objects to be "composed" into larger ones. For example, in this case, what does it *mean* to combine several MD5 sums? The good news is that you can affect how Graph forms these "super components". Look for "super_component" in the documentation. I have now fixed all the bugs shown by the Graph-MD5.t. I have still to look at a SP_Dijkstra() problem another user is seeing.
  Tue May 30 13:15:29 2006 jhi [...] iki.fi - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Tue, 30 May 2006 20:14:41 +0300
To: bug-Graph [...] rt.cpan.org
From: Jarkko Hietaniemi <jhietaniemi [...] gmail.com>
Show quoted text
> osborne1@optonline.net via RT wrote:
>> Queue: Graph >> Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > >> >> Jarrko, >> >> I'm attaching a *t file that has some of my tests on refvertexing. Most
> > Thanks! Do you mind if I "borrow" these sets?
s/sets/tests/ Show quoted text
>> methods tested work, but a couple of methods don't (and I'm not sure if my >> usage of connected_graph() is correct).
  Tue May 30 14:09:31 2006 osborne1 [...] optonline.net - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Tue, 30 May 2006 14:08:39 -0400
To: bug-Graph [...] rt.cpan.org
From: Brian Osborne <osborne1 [...] optonline.net>
Please do! On 5/30/06 1:12 PM, "jhi@iki.fi via RT" <bug-Graph@rt.cpan.org> wrote: Show quoted text
> Thanks! Do you mind if I "borrow" these sets?
  Wed May 31 16:02:35 2006 jhi [...] iki.fi - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Wed, 31 May 2006 23:02:15 +0300
To: bug-Graph [...] rt.cpan.org
From: Jarkko Hietaniemi <jhi [...] iki.fi>
Graph 0.74 uploaded to CPAN.
  Wed May 31 21:48:00 2006 osborne1 [...] optonline.net - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Wed, 31 May 2006 21:46:46 -0400
To: bug-Graph [...] rt.cpan.org
From: Brian Osborne <osborne1 [...] optonline.net>
Jarkko, I'm missing something - where can I find .74? Not at http://search.cpan.org/~jhi/Graph/.... Brian O. On 5/31/06 4:02 PM, "jhi@iki.fi via RT" <bug-Graph@rt.cpan.org> wrote: Show quoted text
> > <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > > > Graph 0.74 uploaded to CPAN. > > > >
  Thu Jun 01 00:51:45 2006 jhi [...] iki.fi - Correspondence added
Subject: Re: [rt.cpan.org #19480] articulation_points stalls
Date: Thu, 01 Jun 2006 07:51:05 +0300
To: bug-Graph [...] rt.cpan.org
From: Jarkko Hietaniemi <jhi [...] iki.fi>
osborne1@optonline.net via RT wrote: Show quoted text
> Queue: Graph > Ticket <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > > > Jarkko, > > I'm missing something - where can I find .74? Not at > http://search.cpan.org/~jhi/Graph/....
It can take a few hours to percolate. Show quoted text
> Brian O. > > > On 5/31/06 4:02 PM, "jhi@iki.fi via RT" <bug-Graph@rt.cpan.org> wrote: >
>> <URL: http://rt.cpan.org/Ticket/Display.html?id=19480 > >> >> Graph 0.74 uploaded to CPAN. >> >> >> >>
> > > >
  Wed Jun 28 15:33:41 2006 JHI [...] cpan.org - Correspondence added
Should be resolved by 0.74.
  Wed Jun 28 15:33:45 2006 JHI [...] cpan.org - Status changed from 'open' to 'resolved'