[Bioperl-l] error installing bioperl-db

Wed Jul 20 12:33:50 EDT 2005

First off, the bioperl-microarray mailing list has little to do with  
this topic. The appropriate list is bioperl-l to which you posted  
first. You can find the page to subscribe at www.bioperl.org.

As for your error report, seeing an error in the tests is usually not a  
good sign. You can force an install but there's likely a problem that  
needs to be fixed. Here, in Postgresql the first failed statement  
invalidates the entire transaction and no other SQL command can succeed  
until the transaction is rolled back. To deal with this the Postgresql  
version of the schema defines 'rules' that do lookups to prevent unique  
key clashes.

One of the statements either failed unexpectedly, or it failed when it  
should have been caught by one of the rules.

Which version of Postgresql are you using? Did you download the schema  
from CVS, and were there any errors when you instantiated it?

I'll need to replicate the error before I can judge further what's  
going on.

	-hilmar

On Jul 20, 2005, at 9:17 AM, Andrew Stewart wrote:

> Doh, that was a sloppy overlook on my part.  Thanks for pointing it  
> out.
>
> make test now reports 97% ok with the following error:
> t/03simpleseq.....NOK 33Use of uninitialized value in join or string  
> at /usr/local/bioperl-db/blib/lib/Bio/DB/BioSQL/BaseDriver.pm line  
> 1845.
>
> -------------------- WARNING ---------------------
> MSG: update in Bio::DB::BioSQL::PrimarySeqAdaptor (driver) failed,  
> values were ("NM_003319","","NM_003319","Homo sapiens titin (TTN),  
> transcript variant N2-B, mRNA","3") FKs (2)
> ERROR:  current transaction is aborted, commands ignored until end of  
> transaction block
>
> ---------------------------------------------------
> Use of uninitialized value in join or string at  
> /usr/local/bioperl-db/blib/lib/Bio/DB/BioSQL/BaseDriver.pm line 1845.
> Use of uninitialized value in join or string at  
> /usr/local/bioperl-db/blib/lib/Bio/DB/BioSQL/BaseDriver.pm line 1845.
> Use of uninitialized value in join or string at  
> /usr/local/bioperl-db/blib/lib/Bio/DB/BioSQL/BaseDriver.pm line 1845.
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::BiosequenceAdaptor (driver) failed,  
> values were ("","82027","dna","","") FKs (2)
> ERROR:  current transaction is aborted, commands ignored until end of  
> transaction block
>
> ---------------------------------------------------
> t/03simpleseq.....ok 34/59                                              
>      ------------- EXCEPTION  -------------
> MSG: error while executing statement in  
> Bio::DB::BioSQL::PrimarySeqAdaptor::find_by_unique_key: ERROR:   
> current transaction is aborted, commands ignored until end of  
> transaction block
>
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key  
> /usr/local/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:951
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key  
> /usr/local/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:855
> STACK (eval) t/03simpleseq.t:112
> STACK toplevel t/03simpleseq.t:66
>
> --------------------------------------
> t/03simpleseq.....FAILED tests 32-33, 35, 38-59                         
>             Failed 25/59 tests, 57.63% okay
>
>
> Is this an error I should be worried about or should I go ahead and  
> force make install?
>
>
> Thanks for the help.  Could I be added to this listserv by the way?
>
> -Andrew Stewart
> US Navy BDRD
>
>
>
>
> Hilmar Lapp wrote:
>
>> Did you configure the name of your driver to be 'postgresql'? Is this  
>> a new DBD driver for PostgreSQL? The DBD driver used to be Pg  
>> (DBD::Pg), so bioperl-db just uses the same convention or name.
>>
>> I.e., change postgresql to Pg in your configuration  
>> (t/DBHarness.biosql.conf), unless the DBD driver you are using is  
>> indeed DBD::postgresql.
>>
>> If the DBD driver you are using is indeed DBD::postgresql and not  
>> DBD::Pg then copy Bio/DB/DBI/Pg.pm to Bio/DB/DBI/postgresql.pm and  
>> rename (or copy) the directory Bio/DB/BioSQL/Pg to  
>> Bio/DB/BioSQL/postgresql.
>>
>> Hth,
>>
>>     -hilmar
>>
>> On Jul 19, 2005, at 3:03 PM, Andrew Stewart wrote:
>>
>>> I'm having a problem while trying to install the bioperl-db modules.  
>>>  While trying to run a make test, I get the following error:
>>>
>>> t/01dbadaptor.....ok 1/13                                             
>>>        ------------- EXCEPTION  -------------
>>> *MSG: Failed to load module Bio::DB::DBI::postgresql*. Can't locate  
>>> Bio/DB/DBI/postgresql.pm in @INC (@INC contains: t  
>>> /usr/local/bioperl-db/blib/lib /usr/local/bioperl-db/blib/arch  
>>> /sw/lib/perl5/5.8.1/darwin-thread-multi-2level /sw/lib/perl5/5.8.1  
>>> /sw/lib/perl5 /sw/lib/perl5/darwin /Users/astew/usr/lib  
>>> /System/Library/Perl/5.8.1/darwin-thread-multi-2level  
>>> /System/Library/Perl/5.8.1  
>>> /Library/Perl/5.8.1/darwin-thread-multi-2level /Library/Perl/5.8.1  
>>> /Library/Perl /Network/Library/Perl/5.8.1/darwin-thread-multi-2level  
>>> /Network/Library/Perl/5.8.1 /Network/Library/Perl .) at  
>>> /sw/lib/perl5/5.8.1/Bio/Root/Root.pm line 396.
>>>
>>> STACK Bio::Root::Root::_load_module  
>>> /sw/lib/perl5/5.8.1/Bio/Root/Root.pm:398
>>> STACK Bio::DB::SimpleDBContext::dbi  
>>> /usr/local/bioperl-db/blib/lib/Bio/DB/SimpleDBContext.pm:296
>>> STACK Bio::DB::BioSQL::DBAdaptor::new  
>>> /usr/local/bioperl-db/blib/lib/Bio/DB/BioSQL/DBAdaptor.pm:85
>>> STACK Bio::DB::BioDB::new  
>>> /usr/local/bioperl-db/blib/lib/Bio/DB/BioDB.pm:203
>>> STACK DBTestHarness::get_DBAdaptor t/DBTestHarness.pm:257
>>> STACK DBTestHarness::get_DBContext t/DBTestHarness.pm:272
>>> STACK toplevel t/01dbadaptor.t:23
>>>
>>> --------------------------------------
>>> t/01dbadaptor.....dubious
>>>        Test returned status 2 (wstat 512, 0x200)
>>> DIED. FAILED tests 2-13
>>>        Failed 12/13 tests, 7.69% okay
>>>
>>>
>>> Where am I supposed to find Bio::DB::DBI::postgresql ?
>>>
>>>
>>> -Andrew Stewart
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> 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
-------------------------------------------------------------