[Bioperl-l] Packaging Bio::Ext::HMM for CPAN, was Re: Problems with Bioperl-ext package on WinVista?

[Yee Man Chan]

I tried that sample script that reportedly caused the dpAlign "bug" but I can't reproduced it. All I get is a warning from LocatableSeq.
-------------------------------------------
[ymc at dev Align]$ PERL_DL_NONLAZY=1 /usr/bin/perl "-Iblib/lib" "-Iblib/arch" "-I/home/ymc/bioperl/bioperl-live/trunk" test.pl

--------------------- WARNING ---------------------
MSG: In sequence ABC|9944760 residue count gives end value 101.
Overriding value [104] with value 101 for Bio::LocatableSeq::end().
TTGCCATTCTTTCGAAGCGCATTCCCTCTCGTGGCGCTGGCTTCCAGGATCTTTTGGAAGCGCATTCGACGCAACACACCTGCCCGTTT-GGG-CCGGCCC-AA
---------------------------------------------------
Getting score for ABC|9944760 -> ABC|9986984
= 300
Getting score for ABC|9986984 -> ABC|9944760
= 303
------------------------------------------

Does the test script crash in your machine?

Yee Man

--- On Tue, 8/18/09, Chris Fields <cjfields at illinois.edu> wrote:

> From: Chris Fields <cjfields at illinois.edu>
> Subject: Re: Packaging Bio::Ext::HMM for CPAN, was Re: [Bioperl-l] Problems with Bioperl-ext package on WinVista?
> To: "Robert Buels" <rmb32 at cornell.edu>
> Cc: "Yee Man Chan" <ymc at yahoo.com>, "BioPerl List" <bioperl-l at lists.open-bio.org>
> Date: Tuesday, August 18, 2009, 10:28 PM
> On Aug 18, 2009, at 11:37 PM, Robert
> Buels wrote:
> 
> > Yee Man Chan wrote:
> >> Is it going to be an arrangement similar to
> bioconductor? If so, I suppose then it makes sense. But you
> might want to develop scripts to automatically download and
> install new modules to make it user friendly.
> > Yes, we are probably going to make a Task::BioPerl or
> something similar.
> > 
> >> What do you mean by Bio-Ext is going away? I
> notice quite many people using dpAlign. So if Bio-Ext is
> going away, then at least dpAlign should become another spin
> off.
> > By going away, I meant that everything in there is
> going to be spinned off.  Except modules that are no
> longer maintainable, if there are any in there.
> > 
> > Rob
> 
> dpAlign could become another spinoff, yes, if it's used
> (and works fine).  The problematic code dealt with pSW,
> alignment statistics, and staden io_lib support (the latter
> which is fairly bit rotted now):
> 
> http://bugzilla.open-bio.org/show_bug.cgi?id=2668
> http://bugzilla.open-bio.org/show_bug.cgi?id=1857
> http://bugzilla.open-bio.org/show_bug.cgi?id=2069
> http://bugzilla.open-bio.org/show_bug.cgi?id=2074
> http://bugzilla.open-bio.org/show_bug.cgi?id=2329
> 
> dpAlign has it's own bug:
> 
> http://bugzilla.open-bio.org/show_bug.cgi?id=2384
> 
> chris
>