[Bioperl-l] Cannot make test on bioperl-db
황미녕
mnhwang at kisti.re.kr
Thu Sep 23 20:59:31 EDT 2004
Thanks your comment ^^
I copyed t/DBHarness.conf.example to t/DBHarness.biosql.conf.
--------------------t/DBHarness.biosql.conf------------------------
{
# DBD driver to use - mandatory
'driver' => 'Oracle',
# machine to connect to - mandatory
'host' => '127.0.0.1',
# user to connect to server as - mandatory
'user' => 'sgowner',
# port the server is running on - optional
'port' => '1521',
# Password if needed
'password' => 'sgbio',
# uncomment if no Biosql database exists. This is the Mysql version.
#'schema_sql' => [ '../biosql-schema/sql/biosqldb-mysql.sql'],
# or for the marker database:
#'schema_sql' => [ './sql/markerdb-mysql.sql'],
# Set to the name of your existing Biosql database. If this is not
# set the test scripts will build a temporary database from scratch
# at the beginning and destroy it at the end. Note that if you set
# this the database must exist, or else the tests will fail.
'dbname' => 'biosql',
# The name of the database within bioperl-db (biosql or map)
'database' => 'biosql',
}
----------------------------------------------------------------
version
Oracle: 10.1.0
DBD::Oracle : 1.15
perl :: 5.8.5
DBI - latetest version
OS : redhat 9.1
----------------------------------------------------------------
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/cluster.......ok 5/160
------------- EXCEPTION -------------
MSG: failed to load adaptor driver for class Bio::DB::BioSQL::BioNamespaceAdaptor as well as parents Bio::DB::BioSQL::BasePersistenceAdaptor
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_get_driver_class /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1569
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbd /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1518
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:928
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:856
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:183
STACK Bio::DB::Persistent::PersistentObject::create /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:243
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:170
STACK Bio::DB::Persistent::PersistentObject::create /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:243
STACK toplevel t/cluster.t:35
--------------------------------------
t/cluster.......dubious
Test returned status 2 (wstat 512, 0x200)
Scalar found where operator expected at (eval 154) line 1, near "'int' $__val"
(Missing operator before $__val?)
DIED. FAILED tests 6-160
Failed 155/160 tests, 3.12% okay
t/comment.......ok 2/11
------------- EXCEPTION -------------
MSG: failed to load adaptor driver for class Bio::DB::BioSQL::BioNamespaceAdaptor as well as parents Bio::DB::BioSQL::BasePersistenceAdaptor
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_get_driver_class /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1569
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbd /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1518
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:928
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:856
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:183
STACK Bio::DB::Persistent::PersistentObject::create /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:243
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:170
STACK Bio::DB::Persistent::PersistentObject::create /home/mnhwang/biosql/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:243
STACK toplevel t/comment.t:32
.........
Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 6-52
Failed 47/52 tests, 9.62% okay
Failed Test Stat Wstat Total Fail Failed List of Failed
-------------------------------------------------------------------------------
t/cluster.t 2 512 160 310 193.75% 6-160
t/comment.t 2 512 11 18 163.64% 3-11
t/dbadaptor.t 255 65280 6 4 66.67% 5-6
t/dblink.t 2 512 18 32 177.78% 3-18
t/ensembl.t 2 512 15 26 173.33% 3-15
t/fuzzy2.t 2 512 21 38 180.95% 3-21
t/genbank.t 2 512 18 32 177.78% 3-18
t/locuslink.t 2 512 110 212 192.73% 5-110
t/ontology.t 2 512 302 596 197.35% 5-302
t/remove.t 2 512 59 116 196.61% 2-59
t/seqfeature.t 2 512 48 90 187.50% 4-48
t/simpleseq.t 2 512 59 108 183.05% 6-59
t/species.t 255 65280 65 120 184.62% 6-65
t/swiss.t 2 512 52 94 180.77% 6-52
Failed 14/15 test scripts, 6.67% okay. 898/962 subtests failed, 6.65% okay.
============================================
What am I doing wrong?
mnhwang
----- Original Message -----
From: "Hilmar Lapp" <hlapp at gnf.org>
To: "H29L3g" <mnhwang at kisti.re.kr>
Cc: <bioperl-l at portal.open-bio.org>
Sent: Friday, September 24, 2004 3:20 AM
Subject: Re: [Bioperl-l] Cannot make test on bioperl-db
Looks like you forgot to copy t/DBHarness.conf.example to
t/DBHarness.biosql.conf and edit to set your driver, and login
credentials etc.
Let me know if you did do that and you get the error nonetheless. In
that case, also provide the versions of OS, perl, DBI, DBD::Oracle, and
Oracle.
-hilmar
On Thursday, September 23, 2004, at 01:25 AM, 황미녕 wrote:
>
> I have installed the Oracle version of BioSQL and bioperl-db,
> 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:
>
> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> t/cluster.......driver not set at t/DBTestHarness.pm line 106
> DBTestHarness::driver('DBTestHarness=HASH(0x871cccc)') called
> at t/DBTestHarness.pm line 204
> DBTestHarness::create_db('DBTestHarness=HASH(0x871cccc)')
> called at t/DBTestHarness.pm line 94
> DBTestHarness::new('DBTestHarness','biosql') called at
> t/cluster.t line 19
> t/cluster.......dubious
> Test returned status 255 (wstat 65280, 0xff00)
> Scalar found where operator expected at (eval 154) line 1, near "'int'
> $__val"
> (Missing operator before $__val?)
> DIED. FAILED tests 1-160
> Failed 160/160 tests, 0.00% okay
> t/comment.......driver not set at t/DBTestHarness.pm line 106
> DBTestHarness::driver('DBTestHarness=HASH(0x863fccc)') called
> at t/DBTestHarness.pm line 204
> DBTestHarness::create_db('DBTestHarness=HASH(0x863fccc)')
> called at t/DBTestHarness.pm line 94
> DBTestHarness::new('DBTestHarness','biosql') called at
> t/comment.t line 20
> t/comment.......dubious
> Test returned status 255 (wstat 65280, 0xff00)
> ..............
>
>
> 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,
> mnhwang_______________________________________________
> 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
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