[BioSQL-l] Re: [Bioperl-l] strange error after changing to RC1.5
Scott Cain
cain at cshl.edu
Sun Mar 13 04:11:17 EST 2005
Hilmar,
I sympathize with your frustration, but backing out those changes will
break several tools that I've written for chado/gmod. This is an
area of active development, and users a frequently advised to update
to bioperl-live. Since there are users of that as well, how do we decide
who gets to feel the pain?
Scott
----------------------------------------------------------------------
Scott Cain, Ph. D. cain at cshl.org
GMOD Coordinator, http://www.gmod.org/ (216)392-3087
----------------------------------------------------------------------
On Sat, 12 Mar 2005, Hilmar Lapp wrote:
> My first response to this was a long rant about almost every single one
> of your statements and which may have been mildly entertaining for
> people while the TV is on commercial. In the end I calmed down and
> thought people have probably better things to do than reading my rants
> (should I start a bioperl blog?), so here is the same in a gist and
> without (most of) the rant.
>
> - In my opinion the annotation system is core, like everything is by
> definition that attaches to a Bio::SeqI.
>
> - I'm not ever going to turn away people who took to the code to fill
> gaps or ambiguities in the documentation - API assumptions based on
> what the code did for years count as a binding contract just as
> expressly written contracts do.
>
> - I am strongly opposed to the notion that your customers should to
> the testing for your wild innovations as opposed to yourself doing that
> in advance, regardless of how fast or slow you respond to bug reports;
> people have better things to do than ironing out your revolution.
>
> - I *am* going to back out the changes from the main trunk;
> traditionally, in bioperl the main trunk has *not* been used for wild
> experiments the repercussions of which were not really clear - instead
> people opened their branches for that.
>
> Allen feel free to reintroduce your changes and overloads and all kinds
> of crazy stuff on a branch that you open. We need the main trunk free
> of debris as the road to the next releases to come. Feel free to wreck
> the train elsewhere. People need the bugfixes now and Lincoln's
> additions that aren't in 1.4.x.
>
> Of course, this being a community project, everybody who disagrees
> please feel free to speak up and if people want to stop me I'll be more
> than glad to step down - but then be prepared to step up yourself and
> take care of the mess.
>
> -hilmar
>
> On Friday, March 11, 2005, at 11:36 AM, Allen Day wrote:
>
> > On Fri, 11 Mar 2005, Hilmar Lapp wrote:
> >
> >> I suggest that all the fancy overloading is removed from core bioperl
> >> modules. If we need overloading for stringification or comparison
> >> operators in one or our core modules I think we are making a mistake.
> >
> > The overloading is only there because assumptions have been made that
> > annotations will be strings. This assumption was okay previously
> > becasue
> > the Bio::Annotation* modules were previously "non core" -- there was no
> > unified annotation system in bioperl. Now these modules are being made
> > core, and this is part of the growing pain.
> >
> > I'm doing what I can to address the bug reports related to these
> > changes
> > as they come in, and I don't think anyone will disagree that I'm doing
> > so
> > in a timely manner. However, I cannot fix bugs or field questions on
> > biosql modules and would appreciate some cooperation/assistance from
> > the
> > biosql developers.
> >
> >> This is part of the huge mess introduced when the SeqFeatureI
> >> architecture was carelessly changed days before release. It's a
> >> prototypical example for what not to do in a project that's as widely
> >> used as bioperl.
> >
> > The SeqFeatureI changes were being gradually made in the 1-2 months
> > prior
> > to the 1.5 release. The release was, may I remind you, a *developer*
> > release and not expected to be bug free.
> >
> >> *Every single bit* of those changes need to be rolled back from the
> >> release and if nobody else has done it by then I will do so in two
> >> weeks.
> >
> > Fine for the 1.5.1 branch, although I don't agree that this should be
> > done
> > on the main trunk.
> >
> > -Allen
> >
> >
> >> -hilmar
> >>
> >> On Thursday, March 10, 2005, at 05:57 PM, Allen Day wrote:
> >>
> >>> I'm unable to test the code in PersistentObject.pm as I don't have
> >>> biosql
> >>> set up, but you might try adding this to Reference.pm
> >>>
> >>> use overload 'ne' => sub { "$_[0]" ne "$_[1]" }
> >>>
> >>> Please let me know if this fixes your error and I'll add this 'ne'
> >>> overload to all the Bio::Annotation::* classes on HEAD.
> >>>
> >>> -Allen
> >>>
> >>>
> >>> On Wed, 9 Mar 2005, Daniel Lang wrote:
> >>>
> >>>> Hi,
> >>>> I´m retrieving seq objects from a local biosql db (using the latest
> >>>> cvs
> >>>> verion of bioperl-db) and e.g. writing them with SeqIO. After
> >>>> changing
> >>>> from a cvs version ~ 12/04 to RC1.5 or latest cvs version, I get the
> >>>> following error:
> >>>>
> >>>> Operation `ne': no method found,!!left argument in overloaded
> >>>> package
> >>>> Bio::Annotation::Reference,!!right argument has no overloaded magic
> >>>> at
> >>>> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/Persistent/PersistentObject.pm
> >>>> line 534, <GEN1> line 1.!
> >>>>
> >>>> The module PersistentObject.pm hasn´t changed and in Reference.pm
> >>>> there
> >>>> is only this change:
> >>>>
> >>>> diff bioperl-live-Dec04/Bio/Annotation/Reference.pm
> >>>> bioperl-live/Bio/Annotation/Reference.pm
> >>>> 1c1
> >>>> < # $Id: Reference.pm,v 1.21 2004/08/19 20:13:32 lapp Exp $
> >>>> ---
> >>>>> # $Id: Reference.pm,v 1.22 2005/02/02 22:13:22 allenday Exp $
> >>>> 56c56,57
> >>>> < # use overload '""' => \&as_text;
> >>>> ---
> >>>>> use overload '""' => sub { $_[0]->title || ''};
> >>>>> use overload 'eq' => sub { "$_[0]" eq "$_[1]" };
> >>>>
> >>>> I´ve reversed this, but no positive result - the error remains...
> >>>> Any hints?
> >>>>
> >>>> Thanks in advance,
> >>>> Daniel
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Bioperl-l mailing list
> >>>> Bioperl-l at portal.open-bio.org
> >>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >>>>
> >>> _______________________________________________
> >>> Bioperl-l mailing list
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> >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>>
> >>
> >
> >
> --
> -------------------------------------------------------------
> Hilmar Lapp email: lapp at gnf.org
> GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
>
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