Re: [GUSDEV] PluginError issue

[Mark S. H. <mh...@ug...>]

I'm coming in late to this thread but it looks like you need to  
install the Error module from CPAN.

http://search.cpan.org/~shlomif/Error-0.17008/lib/Error.pm

I had to install version 0.17006, the latest 0.17008 version didn't  
compile for me out of the box.

-M
On Oct 27, 2006, at 8:21 AM, mro...@cs... wrote:

> Steve,
>
> I am sorry to be a pain, but I was wondering if you have received  
> any news
> from John concerning the PluginError.pm
>
> Thank you
>
>
> Michael
>
>
>
>> john-
>>
>> this GUS user, michael, has downloaded and installed the latest GUS.
>>
>> your new PluginError.pm is giving him problems.  see below.
>>
>> steve
>>
>> mro...@cs... wrote:
>>
>>> Steve,
>>>
>>> Thanks for the phone orientation offer, tomorrow will be great, I  
>>> am on
>>> my
>>> way to a 3 hour class.
>>>
>>> In the meantime I run:
>>>
>>>  mrobi002@acrl-linux-1:/home/acrl-storage-1/gusdb-dev/GUS/
>>>  gus_home/lib/perl/GUS/Supported/Plugin 9%
>>>  ga GUS::Supported::Plugin::InsertSequenceFeatures
>>>  --mapFile $HOME/"pseudomonas aeruginosa"/pa01/genbank2gus.xml
>>>  --inputFileOrDir $HOME/"pseudomonas aeruginosa"/pa01/NC_002516.gbk
>>>  --fileFormat genbank
>>>  --extDbName "Pseudomonas_aeruginosa"
>>>  --extDbRlsVer  "1000"
>>>  --soCvsVersion "1.1.4"
>>>  --commit
>>>
>>>
>>> and got:
>>>
>>>  Base class package "Error" is empty.
>>>    (Perhaps you need to 'use' the module which defines that package
>>>    first.)
>>>  at /home/acrl-storage-1/gusdb-dev/GUS/gus_home/
>>>  lib/perl/GUS/PluginMgr/PluginError.pm line 2
>>>
>>>  BEGIN failed--compilation aborted at
>>> /home/acrl-storage-1/gusdb-dev/GUS/
>>>  gus_home/lib/perl/GUS/PluginMgr/PluginError.pm line 2.
>>>
>>>  Compilation failed in require at /home/acrl-storage-1/gusdb-dev/ 
>>> GUS/
>>>  gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 29.
>>>
>>>  BEGIN failed--compilation aborted at
>>> /home/acrl-storage-1/gusdb-dev/GUS/
>>>  gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 29.
>>>
>>>  Compilation failed in require at /home/acrl-storage-1/gusdb-dev/ 
>>> GUS/
>>>  gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 27.
>>>
>>>  BEGIN failed--compilation aborted at
>>> /home/acrl-storage-1/gusdb-dev/GUS/
>>>  gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 27.
>>>
>>>  Compilation failed in require at /home/acrl-storage-1/gusdb-dev/ 
>>> GUS/
>>>  gus_home/bin/ga line 7.
>>>
>>>  BEGIN failed--compilation aborted at
>>> /home/acrl-storage-1/gusdb-dev/GUS/
>>>  gus_home/bin/ga line 7.
>>>
>>>
>>> I examined the errors by looking in the programs and all errors have
>>> something in common:
>>>
>>> use GUS::PluginMgr::GusApplication; #at ga.pm line 7
>>> use GUS::PluginMgr::Plugin;         #at GusApplication.pm line 27
>>> use GUS::PluginMgr::PluginError;    #at Plugin.pm line 29
>>> use base qw(Error);                 #at PluginError.pm line 2
>>>
>>>
>>> It probably is a stupid mistake on my part, but I can not see
>>>
>>> All help will be very much appreciated.
>>>
>>>
>>> Thanks again
>>>
>>> Michael
>>>
>>>
>>>
>>>
>>>
>>>> the only documentation is what you get by running the plugin w/  
>>>> --help
>>>>
>>>> i can (try to) answer questions as they come up.
>>>>
>>>> it may turn out that the best way to proceed is an orientation  
>>>> by phone.
>>>>
>>>> steve
>>>>
>>>> mro...@cs... wrote:
>>>>
>>>>
>>>>
>>>>> Steve,
>>>>>
>>>>> I am almost ready to insert some bacteria sequences from  
>>>>> genebank, and
>>>>> i
>>>>> have some questions.
>>>>>
>>>>> a - i found in the gusdev site the following:
>>>>>
>>>>> From: Steve Fischer <sfischer@pc...> - 2005-08-31 10:32
>>>>> for those of you who are using the beta version of the ISF plugin:
>>>>>  1. i will improve its documentation to indicate what it  
>>>>> expects to
>>>>>     already be in the database:
>>>>>         - SequenceOntology   (InsertSequenceOntology plugin)
>>>>>         - NCBI Taxon   (LoadTaxon plugin)
>>>>>         - External database and release (InsertExternalDatabase  
>>>>> and
>>>>>                                  InsertExternalDatabaseRls  
>>>>> plugins)
>>>>>         - at least one row in SequenceType so you can say what  
>>>>> type of
>>>>>           sequence you are loading (you can use LoadRow plugin for
>>>>> this)
>>>>>
>>>>>  2.  i will improve the error messages so that it better  
>>>>> detects the
>>>>>      absence of these, and makes it more clear what to do.
>>>>>
>>>>> About loading SO:
>>>>>   1. can you send the SO term with definition that is too big?
>>>>>
>>>>>   2. i understand about the rollback.  we have been discussing  
>>>>> how to
>>>>>      undo a plugin.   for now, you need to do it with sql.
>>>>>
>>>>> Thanks for helping us make this plugin better.
>>>>>
>>>>> steve
>>>>>
>>>>> We did a new GUS install two weeks ago and i wonder if this  
>>>>> applies to
>>>>> me,
>>>>> if it does could you tell me where do i find the documentation  
>>>>> that you
>>>>> mention above.
>>>>>
>>>>> b - When I do a search in gusdev for "InsertSequenceFeatures"  
>>>>> or parts
>>>>> of
>>>>> it, i get very little replies and somotimes none. Is there  
>>>>> another way
>>>>> to
>>>>> find all documents in gusdev relating to this.
>>>>>
>>>>> Thank you
>>>>>
>>>>> Michael R
>>>>>
>>>>>
>>>>> --------------------------------------------
>>>>>
>>>>>
>>
>
>
>
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