[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

Nathan Haigh nathanhaigh at ukonline.co.uk
Wed Dec 1 09:37:30 EST 2004 

I tried installing expat on what I thought was a clean Win98 system but I'd actually previously installed ActiveState Perl and most
of BioPerl's Perl dependencies. Using the current 1.95.8 release of expat_win32bin file, I installed to the default location of
c:\Expat-1.95.8\ and no other configuration options were available - I don't know if I need to point XML::Parser to this location
somehow, but when i ran the t\biblio.t test using the current CVS release of BioPerl and all the tests ran fine without any
warnings. So unless XML::Parser is using some other expat-like module/program that was installed by ActiveState Perl, then things
seem to run fine on my setup.

However, I do need to varyfy the following points:
1) Does ActiveState already have an expat like program/module installed, since it comes shipped with XML::Parser as standard?
2) If so, do I need to "tell" XML::Parser to use the expat I just installed rather than the implementation that may be being used in
1?
3) How do I verify that the expat I installed is actually being used?

I'll run a few scenarios over the next few days/week!

Nathan

> -----Original Message-----
> From: Brian Osborne [mailto:brian_osborne at cognia.com]
> Sent: 01 December 2004 14:08
> To: nathanhaigh at ukonline.co.uk; 'Hilmar Lapp'
> Cc: 'Bioperl'
> Subject: RE: [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes
> 
> 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
> > > -------------------------------------------------------------
> > >
> > >
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