[Bioperl-l] bioperl-db make test errors

[Hilmar Lapp]

Both tests pass for me, running against mysql and both the development  
trunk and the 1.4 branch of bioperl.

To exclude the obvious:
	- did you make sure that innodb is enabled in mysql? You have to edit  
the config file to do that. On the mysql prompt, insert a record into  
biodatabase, then issue a rollback. Is the record that you inserted  
still there?

There may have been fixes to the 1.4 branch from me or somebody else  
after the 1.4.0 release that may fix your problems. Try the latest  
download from cvs of the 1.4 branch.

If this doesn't help, run the locuslink.t test in verbose mode and send  
the result to me. You do this by

	$ make test_locuslink TEST_VERBOSE=1

I suspect the species test failure is caused by the previous one  
(although it actually shouldn't; that's why I also suspect that maybe  
you don't have innodb enabled). Make sure your database is empty and  
then run the species test again individually:

	$ make test_species TEST_VERBOSE=1

Let me know what the result is.

	-hilmar

On Thursday, April 15, 2004, at 09:10  AM, Dave Howorth wrote:

> I'm trying to set up bioperl-db and getting some errors in the make  
> test  (full log is below). I just downloaded bioperl-db and biosql,  
> and just upgraded mysql (from 3.23.49). MySQL appears to run OK with  
> some existing databases. I just created a database (biosql_test) for  
> the tests and loaded the biosqldb-mysql.sql schema.
>
> I'm using:
> bioperl 1.4
> bioperl-db (the README says "README,v 1.17 2003/08/22 12:44:23")
> biosql (the README says "README,v 1.4 2003/09/21 05:01:23")
> Perl 5.6.1
> MySQL 4.0.18
> Debian woody with many backports
>
> Does anybody have any idea what is causing the errors?
>
> Cheers, Dave
>
> ----
>
> bioperl-db$ make test
> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib  
> -I/usr/lib/perl/5.6.1 -I/usr/share/perl/5.6.1 -e 'use Test::Harness  
> qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t
> t/cluster.......ok 155/160
> -------------------- WARNING ---------------------
> MSG: failed to store one or more child objects for an instance of  
> class Bio::Cluster::UniGene (PK=1)
> ---------------------------------------------------
> t/cluster.......ok
> t/comment.......ok
> t/dbadaptor.....ok
> t/dblink........ok
> t/ensembl.......ok
> t/fuzzy2........ok
> t/genbank.......ok
> t/locuslink.....NOK 24Can't call method "as_text" on an undefined  
> value at t/locuslink.t line 122, <GEN0> line 1.
> t/locuslink.....FAILED tests 24, 29-110
> 	Failed 83/110 tests, 24.55% okay
> t/ontology......ok
> t/query.........ok
> t/remove........ok
> t/seqfeature....ok
> t/simpleseq.....ok
> t/species.......ok 5/65
> ------------- EXCEPTION  -------------
> MSG: Unique key query in Bio::DB::BioSQL::SpeciesAdaptor returned 2  
> rows instead of 1. Query was [name_class="scientific  
> name",binomial="Homo sapiens"]
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key  
> blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:960
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key  
> blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:856
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create  
> blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:183
> STACK Bio::DB::Persistent::PersistentObject::create  
> blib/lib/Bio/DB/Persistent/PersistentObject.pm:243
> STACK toplevel t/species.t:35
>
> --------------------------------------
> t/species.......dubious
> 	Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 6-65
> 	Failed 60/65 tests, 7.69% okay
> t/swiss.........ok
> Failed Test   Stat Wstat Total Fail  Failed  List of Failed
> ----------------------------------------------------------------------- 
> --------
> t/locuslink.t              110   83  75.45%  24 29-110
> t/species.t    255 65280    65  120 184.62%  6-65
> Failed 2/15 test scripts, 86.67% okay. 143/930 subtests failed, 84.62%  
> okay.
> make: *** [test_dynamic] Error 11
>
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>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------