[maker-devel] Can't call method "start" on an undefined value

[Carson Holt]

 //= is a feature of perl versions 5.10 and above.

You must have an older version of perl.
Just change it to ||= and it will work for older versions.  I'll make that
change to the release as well to make it work with older perl.

Thanks,
Carson




From:  Evan Ernst <eernst at cshl.edu>
Date:  Mon, 26 Mar 2012 16:13:19 -0400
To:  Carson Holt <carsonhh at gmail.com>
Cc:  <maker-devel at googlegroups.com>
Subject:  Re: [maker-devel] Can't call method "start" on an undefined value

Hi Carson,

Line 242 of maker is causing a compilation failure in the version I
downloaded:

241 -> eval "\$ver = \$${name}::VERSION";
242 -> $ver //= 'UNKNOWN';
243 -> $ver = 'UNKNOWN' if($ver =~ /^\-1\,/);

Thanks,
Evan

On Mon, Mar 26, 2012 at 3:06 PM, Evan Ernst <eernst at cshl.edu> wrote:
> Fantastic. Thanks for your help.
> 
> Best,
> Evan
> 
> 
> On Mon, Mar 26, 2012 at 3:05 PM, Carson Holt <carsonhh at gmail.com> wrote:
>> Ok.  This is fixed (along with a few other things), and is available for
>> download as MAKER 2.25.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> From:  Evan <eernst at cshl.edu>
>> Date:  Mon, 26 Mar 2012 09:29:45 -0700 (PDT)
>> To:  <maker-devel at googlegroups.com>
>> Subject:  [maker-devel] Can't call method "start" on an undefined value
>> 
>> Hi,
>> 
>> I'm running maker 2.24-beta. At least 10-15% of scaffolds are failing with
>> the following error:
>> 
>> Preparing evidence for hint based annotation
>> cleaning clusters....
>> total clusters:1 now processing 0
>> in cluster::shadow_cluster...
>> ...finished clustering.
>> cleaning clusters....
>> total clusters:4 now processing 0
>>  ...processing 0 of 3
>>  ...processing 1 of 3
>> total clusters:4 now processing 0
>>  ...processing 0 of 2
>> total clusters:4 now processing 0
>> total clusters:4 now processing 0
>> Can't call method "start" on an undefined valueERROR: Failed while preparing
>> evidence clusters for annotations
>> ERROR: Chunk failed at level:0, tier_type:3
>> FAILED CONTIG:scaffold93.1
>> 
>> ERROR: Chunk failed at level:7, tier_type:0
>> FAILED CONTIG:scaffold93.1
>> 
>> This occurs when running just a single maker instance.
>> 
>> Thanks,
>> Evan
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma
>> ker-devel_yandell-lab.org
> 
> 
> 
> -- 
> Evan Ernst
> Martienssen Lab
> 
> Delbruck #216
> Cold Spring Harbor Laboratory
> 1 Bungtown Rd.
> Cold Spring Harbor, NY 11724
> 



-- 
Evan Ernst
Martienssen Lab

Delbruck #216
Cold Spring Harbor Laboratory
1 Bungtown Rd.
Cold Spring Harbor, NY 11724



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