[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

[Brian Osborne]

Nathan,

I don't know. But if ActiveState can do the equivalent of "force install"
then the answer is "not necessarily".

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Nathan Haigh
Sent: Wednesday, December 01, 2004 8:54 AM
To: 'Brian Osborne'; 'Hilmar Lapp'
Cc: 'Bioperl'
Subject: RE: [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes


Forgive me if I'm being a bit dense! But, if XML::Parser is included in the
ActiveState Perl distribution, doesn't this mean that
expat (or similar) is also installed?

Nathan

> -----Original Message-----
> From: Brian Osborne [mailto:brian_osborne at cognia.com]
> Sent: 01 December 2004 12:58
> To: nathanhaigh at ukonline.co.uk; 'Hilmar Lapp'
> Cc: 'Bioperl'
> Subject: RE: [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes
>
> Nathan,
>
> t/Biblio.t is one.
>
> It tests Bio/Biblio/IO/medlinexml.pm, which uses XML::Parser, which uses
> expat.
>
> Brian O.
>
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Nathan Haigh
> Sent: Wednesday, December 01, 2004 7:21 AM
> To: 'Hilmar Lapp'
> Cc: 'Bioperl'
> Subject: RE: [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes
>
>
> Which BioPerl test(s) should determine if expat is working correctly?
>
> Nathan
>
> > -----Original Message-----
> > From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Hilmar Lapp
> > Sent: 01 December 2004 06:24
> > To: Aaron J. Mackey
> > Cc: Allen Day; Bioperl
> > Subject: Re: [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes
> >
> > Sounds very reasonable Aaron, and thanks for your gentle herding
> > efforts. :-)
> >
> > For the bioperl developers, this will also mean that for the lifetime
> > of the 1.5 branch, efforts should be made to merge fixes applied to the
> > HEAD to the branch right afterwards.
> >
> > 	-hilmar
> >
> > On Monday, November 29, 2004, at 06:07  AM, Aaron J. Mackey wrote:
> >
> > >
> > > Yep, OK, I hear you.  I really thought all this was going to be
> > > contained to Bio::SeqFeature::Annotated, but I see now that with all
> > > sorts of implementation happening in the interfaces (ugh!), this can't
> > > happen.  Woe is me.
> > >
> > > Here's what I'm willing to do to keep Allen from pulling his hair out:
> > > there have been very few changes on the development trunk since RC1
> > > that aren't Annotated.pm-related; therefore, (if this makes sense to
> > > everyone) I will branch 1.5.0 off of RC1 and merge only those patches
> > > that are Annotated.pm-*unrelated* to the 1.5.0 branch.  I will then
> > > tag the branch at RC2 (and similarly tag the HEAD, so that any later
> > > merging can be done relative to those tags).  Make sense?
> > >
> > > Then, the rest of you (Allen, Hilmar, Steffen, etc) need to figure out
> > > the cleanest path for 1.6.0, in which all things may change (with an
> > > eye towards at least some backwards compatibility); my vote would be
> > > that there remain some separation between "heavy" and "light" feature
> > > types.  I don't expect/need my Bio::SeqFeature::Simple to implement
> > > AnnotationCollection!
> > >
> > > Thanks again to everyone; let me know if the CVS plan above sounds
> > > reasonable ...
> > >
> > > -Aaron
> > >
> > > On Nov 28, 2004, at 10:08 PM, Hilmar Lapp wrote:
> > >
> > >> I'm not saying this change of direction may be a show-stopper for any
> > >> dependent package like bioperl-db. All I'm suggesting is let's be
> > >> clear that this *is* a change of direction for a core interface, and
> > >> let's give it some time to phase it in and to iron out wrinkles, both
> > >> on the end of bioperl itself as well as the end of people who write
> > >> software against bioperl. Let's give it some time to see how it
> > >> works, and how it works under stress, before letting it lose on the
> > >> general public who just wanted to get some bugfixes on the 1.4.0
> > >> release or some additional parsers.
> > >
> > > --
> > > Aaron J. Mackey, Ph.D.
> > > Dept. of Biology, Goddard 212
> > > University of Pennsylvania       email:  amackey at pcbi.upenn.edu
> > > 415 S. University Avenue         office: 215-898-1205
> > > Philadelphia, PA  19104-6017     fax:    215-746-6697
> > >
> > >
> > --
> > -------------------------------------------------------------
> > Hilmar Lapp                            email: lapp at gnf.org
> > GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> > -------------------------------------------------------------
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > ---
> > avast! Antivirus: Inbound message clean.
> > Virus Database (VPS): 0449-0, 30/11/2004
> > Tested on: 01/12/2004 07:58:52
> > avast! is copyright (c) 2000-2003 ALWIL Software.
> > http://www.avast.com
> >
> >
>
> ---
> avast! Antivirus: Outbound message clean.
> Virus Database (VPS): 0449-0, 30/11/2004
> Tested on: 01/12/2004 12:21:16
> avast! is copyright (c) 2000-2003 ALWIL Software.
> http://www.avast.com
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>

---
avast! Antivirus: Outbound message clean.
Virus Database (VPS): 0449-0, 30/11/2004
Tested on: 01/12/2004 13:53:41
avast! is copyright (c) 2000-2003 ALWIL Software.
http://www.avast.com




_______________________________________________
Bioperl-l mailing list
Bioperl-l at portal.open-bio.org
http://portal.open-bio.org/mailman/listinfo/bioperl-l