[Bioperl-l] EUtilities Cookbook example fails

[Adam Witney]

Hi Chris,

not sure if I should start a new thread for this, but it is related to  
the EUtilities Cookbook and LinkSet.pm.

There are several references in the Cookbook to the method  
"get_linkname", however this seems to have changed in the recent  
version of LinkSet.pm to "get_link_name". But one reference to the old  
method name still exists in LinkSet.pm, as shown by this patch:

--- /usr/local/lib/perl5/site_perl/5.8.9/Bio/Tools/EUtilities/Link/ 
LinkSet.pm	2009-02-20 12:36:37.000000000 +0000
+++ /Users/adam/Desktop/LinkSet.pm	2009-06-10 13:58:49.000000000 +0100
@@ -220,7 +220,7 @@
  =cut

  sub get_link_name {
-    return ($_[0]->get_linknames)[0];
+    return ($_[0]->get_link_names)[0];
  }

  =head2 get_submitted_ids

If i haven't got this all wrong entirely, I could go through and fix  
the Cookbook entries if that was useful?

adam


On 10 Jun 2009, at 13:28, Chris Fields wrote:

> I can reproduce that; I'll look into it.
>
> chris
>
> On Jun 10, 2009, at 6:19 AM, Adam Witney wrote:
>
>> Hi,
>>
>> I am going through the EUtilities Cookbook, but the last example  
>> (in section 2.3.1) fails with:
>>
>> Can't use an undefined value as an ARRAY reference at /usr/lib/ 
>> perl5/site_perl/5.8.8/Bio/Tools/EUtilities/Link/LinkSet.pm line 470.
>>
>> This is with BioPerl 1.6.0, perl v5.8.8
>>
>> thanks for any help
>>
>> adam
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
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>
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