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This queue is for tickets about the Bio-Phylo CPAN distribution.

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The Basics
Id: 63062
Status: resolved
Priority: 0/
Queue: Bio-Phylo
People
Owner: Nobody in particular
Requestors: par.larsson.ume [...] gmail.com
Cc:
AdminCc:
Bug Information
Severity: (no value)
Broken in: (no value)
Fixed in: (no value)

History Show all quoted text
  Tue Nov 16 16:55:30 2010 par.larsson.ume [...] gmail.com - Ticket created
Subject: is_clade
Date: Tue, 16 Nov 2010 22:55:20 +0100
To: bug-Bio-Phylo [...] rt.cpan.org
From: Pär Larsson <par.larsson.ume [...] gmail.com>
Dear Dr. Vos, I'm Pär Larsson and I work at the Swedish Defence Research Agency, in Umeå, Sweden. I have used bio::phylo for various scripts. I first would like to thank you for providing it! I recently updated our machine and installed the latest version of your modules and now my scripts don't work any longer. I'm not sure if this is due to a mistake on my behalf or if there is a bug, so I'm reluctant to report it as a bug.If it is not a bug, I was hoping that you might be able to point me in the right direction. It is specifically the "is_clade()" function that I'm after, to check for incongruences among my polymorphic sites. Now, however, it complains by saying "Modification of non-creatable array value attempted, subscript -1 at /usr/local/share/perl/5.10.1/Bio/Phylo/Forest/Node.pm line 1165, <DATA> line 1." when I try to execute. sometimes, however, it works - I guess depending on the tips and the tree in question. Is this something that you recognize? Kind regards, Pär Larsson system details: Ubuntu 10.04, 64 bit. v5.10.1 (*) built for x86_64-linux-gnu-thread-multi Linux venter.foi.se 2.6.32-24-generic #42-Ubuntu SMP Fri Aug 20 14:21:58 UTC 2010 x86_64 GNU/Linux -- Pär Larsson Björnvägen 414 906 43 Umeå 090-2056555 070-6189995 -- Pär Larsson Björnvägen 414 906 43 Umeå 090-2056555 070-6189995
  Fri Nov 19 10:24:31 2010 rutgeraldo [...] gmail.com - Correspondence added
Dear Dr. Larsson, I believe I have tracked down the issue. I have uploaded version 0.31 to CPAN, which should fix things. Could you please check if things are working now? Also, I have emailed you separately to ask if you could provide me with an example file that demonstrates the issue (perhaps a script and some sample data). I would like to use this as a regression test to make sure the issue doesn't return in future releases. Is it possible that the set of tips that you pass into the is_clade method contains a root node under some circumstances? It would be the most likely explanation for the faulty behaviour. Best wishes, Rutger Vos On Tue Nov 16 16:55:30 2010, par.larsson.ume@gmail.com wrote: Show quoted text
> Dear Dr. Vos, > > I'm Pär Larsson and I work at the Swedish Defence Research Agency, in Umeå, > Sweden. I have used bio::phylo for various scripts. I first would like to > thank you for providing it! I recently updated our machine and installed > the latest version of your modules and now my scripts don't work any longer. > I'm not sure if this is due to a mistake on my behalf or if there is a bug, > so I'm reluctant to report it as a bug.If it is not a bug, I was hoping that > you might be able to point me in the right direction. > > It is specifically the "is_clade()" function that I'm after, to check for > incongruences among my polymorphic sites. Now, however, it complains by > saying "Modification of non-creatable array value attempted, subscript -1 at > /usr/local/share/perl/5.10.1/Bio/Phylo/Forest/Node.pm line 1165, <DATA> line > 1." when I try to execute. sometimes, however, it works - I guess depending > on the tips and the tree in question. > > Is this something that you recognize? > > > Kind regards, > > Pär Larsson > > system details: > Ubuntu 10.04, 64 bit. > v5.10.1 (*) built for x86_64-linux-gnu-thread-multi > Linux venter.foi.se 2.6.32-24-generic #42-Ubuntu SMP Fri Aug 20 14:21:58 UTC > 2010 x86_64 GNU/Linux > >
  Fri Nov 19 10:24:31 2010 The RT System itself - Status changed from 'new' to 'open'
  Fri Nov 19 10:31:28 2010 par.larsson.ume [...] gmail.com - Correspondence added
Subject: Re: [rt.cpan.org #63062] is_clade
Date: Fri, 19 Nov 2010 16:31:17 +0100
To: bug-Bio-Phylo [...] rt.cpan.org
From: Pär Larsson <par.larsson.ume [...] gmail.com>
Thanks a lot! I will try the new module, and provide you with the script and data asap! //Pär ----------------------------------- Pär Larsson, PhD Research Scientist, Bioinformatics CBRN Defence and Security Swedish Defence Research Agency SE-901 82 Umeå Sweden Phone: +46 90 106789 Cell: +46 70 6189995 Fax: +46 90 106800 2010/11/19 Rutger Vos via RT <bug-Bio-Phylo@rt.cpan.org> Show quoted text
> <URL: https://rt.cpan.org/Ticket/Display.html?id=63062 > > > Dear Dr. Larsson, > > I believe I have tracked down the issue. I have uploaded version 0.31 to > CPAN, which should > fix things. Could you please check if things are working now? Also, I have > emailed you > separately to ask if you could provide me with an example file that > demonstrates the issue > (perhaps a script and some sample data). I would like to use this as a > regression test to make > sure the issue doesn't return in future releases. > > Is it possible that the set of tips that you pass into the is_clade method > contains a root node > under some circumstances? It would be the most likely explanation for the > faulty behaviour. > > Best wishes, > > Rutger Vos > > On Tue Nov 16 16:55:30 2010, par.larsson.ume@gmail.com wrote:
> > Dear Dr. Vos, > > > > I'm Pär Larsson and I work at the Swedish Defence Research Agency, in
> Umeå,
> > Sweden. I have used bio::phylo for various scripts. I first would like to > > thank you for providing it! I recently updated our machine and installed > > the latest version of your modules and now my scripts don't work any
> longer.
> > I'm not sure if this is due to a mistake on my behalf or if there is a
> bug,
> > so I'm reluctant to report it as a bug.If it is not a bug, I was hoping
> that
> > you might be able to point me in the right direction. > > > > It is specifically the "is_clade()" function that I'm after, to check for > > incongruences among my polymorphic sites. Now, however, it complains by > > saying "Modification of non-creatable array value attempted, subscript -1
> at
> > /usr/local/share/perl/5.10.1/Bio/Phylo/Forest/Node.pm line 1165, <DATA>
> line
> > 1." when I try to execute. sometimes, however, it works - I guess
> depending
> > on the tips and the tree in question. > > > > Is this something that you recognize? > > > > > > Kind regards, > > > > Pär Larsson > > > > system details: > > Ubuntu 10.04, 64 bit. > > v5.10.1 (*) built for x86_64-linux-gnu-thread-multi > > Linux venter.foi.se 2.6.32-24-generic #42-Ubuntu SMP Fri Aug 20 14:21:58
> UTC
> > 2010 x86_64 GNU/Linux > > > >
> > > >
-- Pär Larsson Björnvägen 414 906 43 Umeå 090-2056555 070-6189995
  Thu Nov 25 02:26:32 2010 petter.lindgren [...] foi.se - Correspondence added
CC: Pär Larsson <par.larsson.ume [...] gmail.com>
Subject: SV: [rt.cpan.org #63062] is_clade
Date: Thu, 25 Nov 2010 08:26:18 +0100
To: "bug-Bio-Phylo [...] rt.cpan.org" <bug-Bio-Phylo [...] rt.cpan.org>
From: Petter Lindgren <petter.lindgren [...] foi.se>
Thanks Rutger, the update fixed the problem. Best regards Petter ============================================= Petter Lindgren M.Sc. Bioinformatics FOI - Swedish Defence Research Agency CBRN Defence and Security Cementvägen 20 901 82 UMEÅ SWEDEN Phone: +4690 10 66 73 ============================================= Show quoted text
________________________________ Från: Pär Larsson [mailto:par.larsson.ume@gmail.com] Skickat: den 19 november 2010 16:29 Till: Petter Lindgren Ämne: Re: [rt.cpan.org #63062] is_clade 2010/11/19 Rutger Vos via RT <bug-Bio-Phylo@rt.cpan.org<mailto:bug-Bio-Phylo@rt.cpan.org>> <URL: https://rt.cpan.org/Ticket/Display.html?id=63062 > Dear Dr. Larsson, I believe I have tracked down the issue. I have uploaded version 0.31 to CPAN, which should fix things. Could you please check if things are working now? Also, I have emailed you separately to ask if you could provide me with an example file that demonstrates the issue (perhaps a script and some sample data). I would like to use this as a regression test to make sure the issue doesn't return in future releases. Is it possible that the set of tips that you pass into the is_clade method contains a root node under some circumstances? It would be the most likely explanation for the faulty behaviour. Best wishes, Rutger Vos On Tue Nov 16 16:55:30 2010, par.larsson.ume@gmail.com<mailto:par.larsson.ume@gmail.com> wrote:
> Dear Dr. Vos, > > I'm Pär Larsson and I work at the Swedish Defence Research Agency, in Umeå, > Sweden. I have used bio::phylo for various scripts. I first would like to > thank you for providing it! I recently updated our machine and installed > the latest version of your modules and now my scripts don't work any longer. > I'm not sure if this is due to a mistake on my behalf or if there is a bug, > so I'm reluctant to report it as a bug.If it is not a bug, I was hoping that > you might be able to point me in the right direction. > > It is specifically the "is_clade()" function that I'm after, to check for > incongruences among my polymorphic sites. Now, however, it complains by > saying "Modification of non-creatable array value attempted, subscript -1 at > /usr/local/share/perl/5.10.1/Bio/Phylo/Forest/Node.pm line 1165, <DATA> line > 1." when I try to execute. sometimes, however, it works - I guess depending > on the tips and the tree in question. > > Is this something that you recognize? > > > Kind regards, > > Pär Larsson > > system details: > Ubuntu 10.04, 64 bit. > v5.10.1 (*) built for x86_64-linux-gnu-thread-multi > Linux venter.foi.se<http://venter.foi.se> 2.6.32-24-generic #42-Ubuntu SMP Fri Aug 20 14:21:58 UTC > 2010 x86_64 GNU/Linux > >
-- Pär Larsson Björnvägen 414 906 43 Umeå 090-2056555 070-6189995
  Fri Nov 26 20:10:27 2010 rutgeraldo [...] gmail.com - Status changed from 'open' to 'resolved'