[Bioperl-l] Problems with bioperl-db

[Elia Stupka]

> I'm trying to compile bioperl-db package, and fail on most of the tests. 
> BioPerl version that I've got is 0.9.0 and I'm running it on MacOS X 10.0.
> 4.

Alex,
It turns out that bioperl-db has had little attention recently, I am
really glad you wrote, and I am working hard on getting back all tests to
pass, will write as soon as it's over. :)

Elia

> 
> MySQL server seems to be working OK.
> I have edited the DBHarness.conf to reflect my local settings.
> 
> Can anybody please give me a hint on what am I doing wrong?
> 
> Thank you!
> 
> Here is what I get:
> 
> anz% make test
> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib 
> -I/System/Library/Perl/darwin -I/System/Library/Perl -e 'use Test::Harness 
> qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t
> t/comment...........ok
> t/dbadaptor.........ok
> t/dblink............ok
> t/ePCRdb............ok 1/5Can't locate object method "new" via package "Bio:
> :DB::SQL::DBAdaptor" at t/DBTestHarness.pm line 227.
> t/ePCRdb............dubious
>          Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 2-5
>          Failed 4/5 tests, 20.00% okay
> t/ensembl...........ok 4/14-------------------- 
> EXCEPTION --------------------
> MSG: Could not find db for name genbank
> STACK Bio::DB::SQL::BioDatabaseAdaptor::fetch_by_name blib/lib/Bio/DB/SQL/
> BioDatabaseAdaptor.pm:121
> STACK Bio::DB::SQL::BioDatabaseAdaptor::fetch_by_name_store_if_needed blib/
> lib/Bio/DB/SQL/BioDatabaseAdaptor.pm:90
> STACK toplevel t/ensembl.t:39
> -------------------------------------------
> t/ensembl...........dubious
>          Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 5-14
>          Failed 10/14 tests, 28.57% okay
> t/map...............ok 1/15Can't locate object method "new" via package 
> "Bio::DB::SQL::DBAdaptor" at t/DBTestHarness.pm line 227.
> t/map...............dubious
>          Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 2-15
>          Failed 14/15 tests, 6.67% okay
> t/marker............ok 1/34Can't locate object method "new" via package 
> "Bio::DB::SQL::DBAdaptor" at t/DBTestHarness.pm line 227.
> t/marker............dubious
>          Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 2-34
>          Failed 33/34 tests, 2.94% okay
> t/seqfeature........ok 3/9Can't locate object method "is_remote" via 
> package "Bio::Location::Simple" at blib/lib/Bio/DB/SQL/SeqLocationAdaptor.
> pm line 212.
> t/seqfeature........dubious
>          Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 4-9
>          Failed 6/9 tests, 33.33% okay
> t/seqfeaturekey.....ok
> t/seqlocation.......ok 3/10Can't locate object method "is_remote" via 
> package "Bio::Location::Simple" at blib/lib/Bio/DB/SQL/SeqLocationAdaptor.
> pm line 212.
> t/seqlocation.......dubious
>          Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 4-10
>          Failed 7/10 tests, 30.00% okay
> t/simpleseq.........ok 4/20-------------------- 
> EXCEPTION --------------------
> MSG: Could not find db for name genbank
> STACK Bio::DB::SQL::BioDatabaseAdaptor::fetch_by_name blib/lib/Bio/DB/SQL/
> BioDatabaseAdaptor.pm:121
> STACK Bio::DB::SQL::BioDatabaseAdaptor::fetch_by_name_store_if_needed blib/
> lib/Bio/DB/SQL/BioDatabaseAdaptor.pm:90
> STACK toplevel t/simpleseq.t:40
> -------------------------------------------
> t/simpleseq.........dubious
>          Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 5-20
>          Failed 16/20 tests, 20.00% okay
> t/species...........ok
> t/swiss.............ok 4/16-------------------- 
> EXCEPTION --------------------
> MSG: Could not find db for name swissprot
> STACK Bio::DB::SQL::BioDatabaseAdaptor::fetch_by_name blib/lib/Bio/DB/SQL/
> BioDatabaseAdaptor.pm:121
> STACK Bio::DB::SQL::BioDatabaseAdaptor::fetch_by_name_store_if_needed blib/
> lib/Bio/DB/SQL/BioDatabaseAdaptor.pm:90
> STACK toplevel t/swiss.t:38
> -------------------------------------------
> t/swiss.............dubious
>          Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 5-16
>          Failed 12/16 tests, 25.00% okay
> Failed Test  Status Wstat Total Fail  Failed  List of failed
> -------------------------------------------------------------------------------
> t/ePCRdb.t      255 65280     5    4  80.00%  2-5
> t/ensembl.t     255 65280    14   10  71.43%  5-14
> t/map.t         255 65280    15   14  93.33%  2-15
> t/marker.t      255 65280    34   33  97.06%  2-34
> t/seqfeature.t  255 65280     9    6  66.67%  4-9
> t/seqlocation.t 255 65280    10    7  70.00%  4-10
> t/simpleseq.t   255 65280    20   16  80.00%  5-20
> t/swiss.t       255 65280    16   12  75.00%  5-16
> Failed 8/13 test scripts, 38.46% okay. 102/156 subtests failed, 34.62% okay.
> make: *** [test_dynamic] Error 2
> 
> 
> ---------------------------------------------------------------------------
> Alex Zelensky,
> Computational Molecular Biology & Drug Design Group
> John Curtin School of Medical Research
> PO Box 334, Canberra ACT 2601
> Phone: +61-2-6125-8303
> Fax: +61-2-6125-0415
> ---------------------------------------------------------------------------
> 

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