[Bioperl-l] strange error after changing to RC1.5

Hilmar Lapp hlapp at gmx.net
Sun Mar 13 05:06:46 EST 2005 

Can you formulate as a test case how you use the API such it depends on  
those changes that I may be targeting?

Or are these test cases in a gmod package that can be set up reasonably  
simple?

Are you sure that what you depend on are the changes to the  
Bio::SeqFeatureI and Bio::Annotation::* modules? If it's only  
SeqFeature::Annotated, my plan was to leave that as much intact as  
possible.

	-hilmar

On Sunday, March 13, 2005, at 01:11  AM, Scott Cain wrote:

> 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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>>>>>
>>>>>
>>>>
>>>
>>>
>> -- 
>> -------------------------------------------------------------
>> Hilmar Lapp                            email: lapp at gnf.org
>> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>> -------------------------------------------------------------
>>
>>
>>
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>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------

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