From mnhwang at kisti.re.kr  Thu Sep 23 04:41:54 2004
From: mnhwang at kisti.re.kr (=?ks_c_5601-1987?B?yLK5zLPn?=)
Date: Thu Sep 23 10:18:49 2004
Subject: [BioSQL-l] Cannot make test on bioperl-db
Message-ID: <000601c4a149$2dbb4a30$78ebb796@danji>


Hello. 

I had some problem in installing BioSQL/BioPerl, and I have been searching the web for the solution. 
And, finally, I found your posting about the problems of BioSQL/BioPerl installation. 
Your article exactly describes my problem, but I found no one have answered to your question. W
ould you please let me know if you found the solution for the problem.

Thanks
Mi-Nyeong Hwang 



--------------------------------------------------------------------------------

 
Apologies for the cross-post but I am not sure if it is BioSQL or
BioPerl at fault here.

I have installed the Oracle version of BioSQL and bioperl-db as
downloaded last week, and they compile and install fine. However, make
test on bioperl-db fails miserably with hundreds of messages similar to
the following on virtually every module:

---SNIP---
bifo6.agresearch.co.nz> make test
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
"test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/cluster.......ok 155/160DBD::Oracle::st execute failed: ORA-00001:
unique constraint (SGOWNER.XPKBIOENTRY_QUALIFIER_ASSOC) violated (DBD
ERROR: OCIStmtExecute) [for Statement "INSERT INTO
bioentry_qualifier_value (ent_oid, trm_oid, value, rank) VALUES (?, ?,
?, ?)" with ParamValues: :p3='ORG=Escherischia coli; PROTGI=8928262;
PROTID=Ec_pid; PCT=24; ALN=254', :p1='417', :p4=1, :p2='421'] at
/usr/users/oracle/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdapt
or.pm line 418, <GEN0> line 1.
DBD::Oracle::st execute failed: ORA-00001: unique constraint
(SGOWNER.XPKBIOENTRY_QUALIFIER_ASSOC) violated (DBD ERROR:
OCIStmtExecute) [for Statement "INSERT INTO bioentry_qualifier_value
(ent_oid, trm_oid, value, rank) VALUES (?, ?, ?, ?)" with ParamValues:
:p3='ORG=Homo sapiens; PROTGI=114238; PROTID=sp:P11245; PCT=100;
ALN=289', :p1='417', :p4=2, :p2='421'] at
/usr/users/oracle/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdapt
or.pm line 418, <GEN0> line 1.
DBD::Oracle::st execute failed: ORA-00001: unique constraint
(SGOWNER.XPKBIOENTRY_QUALIFIER_ASSOC) violated (DBD ERROR:
OCIStmtExecute) [for Statement "INSERT INTO bioentry_qualifier_value
(ent_oid, trm_oid, value, rank) VALUES (?, ?, ?, ?)" with ParamValues:
:p3='ORG=Mus musculus; PROTGI=1703436; PROTID=sp:P50295; PCT=74;
ALN=289', :p1='417', :p4=3, :p2='421'] at
/usr/users/oracle/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdapt
or.pm line 418, <GEN0> line 1.
DBD::Oracle::st execute failed: ORA-00001: unique constraint
(SGOWNER.XPKBIOENTRY_QUALIFIER_ASSOC) violated (DBD ERROR:
OCIStmtExecute) [for Statement "INSERT INTO bioentry_qualifier_value
(ent_oid, trm_oid, value, rank) VALUES (?, ?, ?, ?)" with ParamValues:
:p3='ORG=Rattus norvegicus; PROTGI=1703437; PROTID=sp:P50298; PCT=73;
ALN=289', :p1='417', :p4=4, :p2='421'] at
/usr/users/oracle/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdapt
or.pm line 418, <GEN0> line 1.
---SNIP---

My installation includes the text indexer option, and I have run the
script to load the taxon information (which incidentally took almost 20
hours to run on a three-processor Compaq Alpha with 11 gigs of RAM -
that's also a bit of a worry, surely?).

The only tables with any data in (I have checked this) are taxon and
taxon_name. The test failed before I loaded the taxon information in
exactly the same way as it does now.

I am wary of wasting time trying to load real data if the test fails
like this - is it a 'fatal' problem or can I ignore it and load real
data anyway?

Any idea what's going on here? I can't figure it out.

cheers,
Richard

---
Richard Holland
Bioinformatics Database Developer
ITS, Agresearch Invermay x3279