[Bioperl-l] Deep recursion on subroutine
Jason Stajich
jason.stajich at duke.edu
Wed Nov 30 17:10:01 EST 2005
Without an actual example tree it is hard to really help you very much.
A simple code example which can reproduce the problem and the
offending tree should be submitted (please attach and don't just
paste the datafile into the comment) as part of the bug report.
http://bugzilla.open-bio.org/
You should also mention what version of Bioperl you are using.
-jason
On Nov 30, 2005, at 4:46 PM, Qunfeng wrote:
> Hi,
>
> I am using bioperl (5.8.0, linux) to work on a UPGMA tree (newick
> format, generated by PHYLIP). My code works well on a small tree.
> However, when I applied it to a big (ugly) tree, it produces the
> following error msg. Has anybody encountered a similar problem? Is
> this triggered by any invalid part of my tree? Thanks!
>
> Qunfeng
> ===========Error message begins =====================
> Deep recursion on subroutine
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at /
> usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at /
> usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at /
> usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at /
> usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at /
> usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, <GEN0>
> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, <GEN0> line 1.
> Deep recursion on subroutine
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine
> "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/
> 5.8.0/Bio/Tree/NodeI.pm line 172, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/
> perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, <GEN0> line 1.
> =========Error msg ends==============================================
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
--
Jason Stajich
Duke University
http://www.duke.edu/~jes12
More information about the Bioperl-l
mailing list