Olivier BUHARD | 27 Mar 13:24 2014
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Re: New to BioPerl ... part II

Hi Hilmar,

I tried again after installing some of the optional modules, but that 
didn't change anything as you expected.
Below are the messages I get will running  >perl Build test for 
BioPerl-1.6.923: (and just exceptions and warnings)

t/Assembly/core.t ...................... 139/890 Can't do inplace edit 
without backup at Bio/Root/IO.pm line 570.
# Looks like you planned 890 tests but ran 246.
# Looks like your test exited with 25 just after 246.
t/Assembly/core.t ...................... Dubious, test returned 25 
(wstat 6400,0x1900)
Failed 644/890 subtests
...
t/LocalDB/BioDBGFF.t ................... 2/275
You are loading a Bio::DB::GFF database with GFF3 formatted data.
While this will likely work fine, the Bio::DB::GFF schema does not 
always faithfully capture the complexity represented in GFF3 files.
Unless you have a specific reason for using Bio::DB::GFF, we suggest 
that you use a Bio::DB::SeqFeature::Store database and its corresponding
loader, bp_seqfeature_load.pl.
t/LocalDB/BioDBGFF.t ................... ok
...
t/LocalDB/transfac_pro.t ............... 5/115 cannot unlink file for 
C:\DOCUME~1\Olivier\LOCALS~1\Temp\N0r8T9tMKD\id2names: Permission denied 
at C:/strawberry/perl/lib/File/Temp.pm line 784.
cannot unlink file for 
C:\DOCUME~1\Olivier\LOCALS~1\Temp\N0r8T9tMKD\nodes: Permission denied at 
C:/strawberry/perl/lib/File/Temp.pm line 784.
cannot remove directory for 
C:/DOCUME~1/Olivier/LOCALS~1/Temp/N0r8T9tMKD: Directory not empty at 
C:/strawberry/perl/lib/File/Temp.pm line 784.
...
t/Root/RootIO.t ........................ 1/77
#   Failed test 'executable file'
#   at t/Root/RootIO.t line 59.
Can't do inplace edit without backup at Bio/Root/IO.pm line 570.
Error removing C:/DOCUME~1/Olivier/LOCALS~1/Temp/LyN7tRQ677 at 
C:/strawberry/perl/lib/File/Temp.pm line 762.
# Looks like you planned 77 tests but ran 45.
# Looks like you failed 1 test of 45 run.
# Looks like your test exited with 25 just after 45.
t/Root/RootIO.t ........................ Dubious, test returned 25 
(wstat 6400,0x1900)
Failed 33/77 subtests
...
t/SearchIO/hmmer.t ..................... 292/327 'cat' n'est pas reconnu 
en tant que commande interne ou externe, un programme exécutable ou un 
fichier de commandes.
#   Failed test 'Check for the correct result reference type'
#   at t/SearchIO/hmmer.t line 637.
#          got: ''
#     expected: 'Bio::Search::Result::HMMERResult'
Can't call method "num_hits" on an undefined value at t/SearchIO/hmmer.t 
line 641.
# Looks like you planned 327 tests but ran 298.
# Looks like you failed 1 test of 298 run.
# Looks like your test exited with 256 just after 298.
t/SearchIO/hmmer.t ..................... Failed 30/327 subtests
...
t/SeqIO/fasta.t ........................ 1/22 Subroutine _initialize 
redefined at Bio\SeqIO\fasta.pm line 85.
Subroutine next_seq redefined at Bio\SeqIO\fasta.pm line 119.
Subroutine write_seq redefined at Bio\SeqIO\fasta.pm line 199.
Subroutine width redefined at Bio\SeqIO\fasta.pm line 289.
Subroutine block redefined at Bio\SeqIO\fasta.pm line 310.
Subroutine preferred_id_type redefined at Bio\SeqIO\fasta.pm line 335.
t/SeqIO/fasta.t ........................ ok
...
t/Tools/Run/WBCommandExts.t ............ 1/25
#   Failed test 'find in syspath'
#   at t/Tools/Run/WBCommandExts.t line 64.
# Looks like you failed 1 test of 25.
t/Tools/Run/WBCommandExts.t ............ Dubious, test returned 1 (wstat 
256, 0x100)
Failed 1/25 subtests
         (1 TODO test unexpectedly succeeded)




For BioPerl-DB-1.006900.tar.gz: (not reported all the subroutine 
redefinition in Species.pm, they are many...)
I get tons of warnings. I don't put all here, just the "first"one. If 
you really need, I can send you the whole list but it is surely hundreds 
on lines!

t\02species.t ..... 5/67
#   Failed test at t\02species.t line 72.
Can't call method "primary_key" on an undefined value at t\02species.t 
line 73.
# Looks like you planned 67 tests but ran 44.
# Looks like you failed 1 test of 44 run.
# Looks like your test exited with 2 just after 44.
t\02species.t ..... Dubious, test returned 2 (wstat 512, 0x200)
Failed 24/67 subtests
t\03simpleseq.t ... 15/70 Can't call method "length" on an undefined 
value at t\03simpleseq.t line 104.
# Looks like you planned 70 tests but ran 42.
t\03simpleseq.t ... Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 28/70 subtests
...
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Unique key query in Bio::DB::BioSQL::SimpleValueAdaptor returned 2 
rows instead of 1. Query was [tagname="keyword",ontology="1"]
STACK: Error::throw
STACK: Bio::Root::Root::throw 
C:/strawberry/perl/site/lib/Bio\Root\Root.pm:486
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:978
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:873
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:195
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264
STACK: Bio::DB::Persistent::PersistentObject::store 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio/DB/Persistent/PersistentObject.pm:284
STACK: Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio\DB\BioSQL\AnnotationCollectionAdaptor.pm:230
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:227
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264
STACK: Bio::DB::Persistent::PersistentObject::store 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio/DB/Persistent/PersistentObject.pm:284
STACK: Bio::DB::BioSQL::SeqAdaptor::store_children 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio\DB\BioSQL\SeqAdaptor.pm:237
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:227
STACK: Bio::DB::Persistent::PersistentObject::create 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio/DB/Persistent/PersistentObject.pm:257
STACK: t\04swiss.t:28
-----------------------------------------------------------
# Looks like you planned 55 tests but ran 8.
# Looks like your test exited with 255 just after 8.
t\04swiss.t ....... Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 47/55 subtests
...
t\05seqfeature.t .. 6/52
--------------------- WARNING ---------------------
MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement 
execution: Le champ 'term_id' ne peut Ûtre vide (null)
         name: INSERT ASSOC [2] 
Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
         values: FK[Bio::SeqFeature::Generic]:2, 
FK[Bio::Annotation::SimpleValue]:, value:"1", rank:"1"
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement 
execution: Le champ 'term_id' ne peut Ûtre vide (null)
         name: INSERT ASSOC [2] 
Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
         values: FK[Bio::SeqFeature::Generic]:2, 
FK[Bio::Annotation::SimpleValue]:, rank:"1", 
value:"MIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTVQNCD
LEQQSIVHIVQRPRRRSHETNASGGDEPQSTSEGSIWESRSLTRVDLSSHTLPVDSVGLAVILDTDSKRDSEAARGPVKP
TYNSFFIYCKGPCHKVQPGKLRVQCGTCKQATLTLAQGPSCWDDVLIPNRMSGECQSPDCPGTRAEFFFKCGAHPTSDKD
TSVALNLITSNRRSIPCIACTDVRSPVLVFQCNHRHVICLDCFHLYCVTRLNDRQFVHDAQLGYSLPCVAGCPNSLIKEL
HHFRILGEEQYTRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEQGQRKVTCEGGNGLGCGFVFCRDCKEAYHEGDCDSLL
EPSGATSQAYRVDKRAAEQARWEEASKETIKKTTKPCPRCNVPIEKNGGCMHMKCPQPQCKLEWCWNCGCEWNRACMGDH
WFDV"
---------------------------------------------------
t\05seqfeature.t .. 7/52
--------------------- WARNING ---------------------
MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement 
execution: Le champ 'term_id' ne peut Ûtre vide (null)
         name: INSERT ASSOC [2] 
Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
         values: FK[Bio::SeqFeature::Generic]:3, 
FK[Bio::Annotation::SimpleValue]:, value:"18", rank:"1"
---------------------------------------------------

#   Failed test at t\05seqfeature.t line 69.
#          got: '1'
#     expected: '2'

--------------------- WARNING ---------------------
MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement 
execution: Le champ 'term_id' ne peut Ûtre vide (null)
         name: INSERT ASSOC [2] 
Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
         values: FK[Bio::SeqFeature::Generic]:3, 
FK[Bio::Annotation::SimpleValue]:, value:"12345", rank:"1"
---------------------------------------------------

#   Failed test at t\05seqfeature.t line 87.
#          got: '1'
#     expected: 'something else'

#   Failed test at t\05seqfeature.t line 89.
#          got: '1'
#     expected: 'value for tag13'

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Unique key query in Bio::DB::BioSQL::TermAdaptor returned 2 rows 
instead of
  1. Query was [name="some-source",ontology="4"]
STACK: Error::throw
STACK: Bio::Root::Root::throw 
C:/strawberry/perl/site/lib/Bio\Root\Root.pm:486
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:978
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:873
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:195
STACK: Bio::DB::Persistent::PersistentObject::create 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio/DB/Persistent/PersistentObject.pm:257
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:182
STACK: Bio::DB::Persistent::PersistentObject::create 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio/DB/Persistent/PersistentObject.pm:257
STACK: t\05seqfeature.t:96
-----------------------------------------------------------
# Looks like you planned 52 tests but ran 31.
# Looks like you failed 3 tests of 31 run.
t\05seqfeature.t .. Dubious, test returned 3 (wstat 768, 0x300)
Failed 24/52 subtests
...
--------------------- WARNING ---------------------
MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement 
execution: Le champ 'term_id' ne peut Ûtre vide (null)
         name: INSERT ASSOC [2] 
Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
         values: FK[Bio::SeqFeature::Generic]:4, 
FK[Bio::Annotation::SimpleValue]:, rank:"1", value:"taxon:10090"
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: SimpleValueAdaptor::add_assoc: unexpected failure of statement 
execution: Le champ 'term_id' ne peut Ûtre vide (null)
         name: INSERT ASSOC [2] 
Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
         values: FK[Bio::SeqFeature::Generic]:4, 
FK[Bio::Annotation::SimpleValue]:, value:"Mus musculus", rank:"1"
---------------------------------------------------


...

and so on.

...

t\13remove.t ...... 4/61
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Species) failed to insert or to be found by 
unique key
STACK: Error::throw
STACK: Bio::Root::Root::throw 
C:/strawberry/perl/site/lib/Bio\Root\Root.pm:486
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:219
STACK: Bio::DB::Persistent::PersistentObject::create 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio/DB/Persistent/PersistentObject.pm:257
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:182
STACK: Bio::DB::Persistent::PersistentObject::create 
C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\blib\lib/Bio/DB/Persistent/PersistentObject.pm:257
STACK: t\13remove.t:29
-----------------------------------------------------------
# Looks like you planned 61 tests but ran 9.
t\13remove.t ...... Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 52/61 subtests
...
t\16obda.t ........ 7/16
--------------------- WARNING ---------------------
MSG: This Perl doesn't implement function getpwuid(), no $HOME
---------------------------------------------------
t\16obda.t ........ ok


I checked my biosql_hs db was empty when I started make test, and I got 
46 records in the all tables at the end. So the database id accessible 
but there is something wrong somewhere. Exceptions about Bio::Root are 
very frequent.

I hope I've sent what you asked for.
I'm installing on my Ubuntu, but the way the things are going I feel 
I'll get troubles too...

Kind regards

Olivier





Le 26/03/2014 15:23, Hilmar Lapp a écrit :
> I can't imagine how the missing dependencies could be the reason, but 
> it is possible that one of them is a false optional, i.e., is given as 
> optional when in reality it is assumed to be installed.
>
> In particular, the fact that many Bioperl-db tests, but not all, seem 
> to be bailing out early on (rather than running through the tests and 
> failing a few) raises alarm. It's possible that this is because of a 
> module loaded in the tests that bail out, and not in those that don't. 
> Can you turn on verbose tests so we see the error message? (I think in 
> the olden days that meant using verbose=1 on the 'make test' command; 
> not sure how this is done now.) Or alternatively, run only one of the 
> tests that bail out.
>
>   -hilmar
>
>
> On Wed, Mar 26, 2014 at 8:50 AM, Olivier BUHARD 
> <Olivier.Buhard <at> inserm.fr <mailto:Olivier.Buhard <at> inserm.fr>> wrote:
>
>     Dear Hilmar,
>
>     I checked and there is nothing in my "biosql_hs" database. I even
>     dropped it and created a new one to be sure and I got errors again.
>     I use phpmyadmin to manage the mysql server on windows xp, so it's
>     easy to verify. All 28 tables of the db have 0 record from the
>     start. Then I run once load_seqdatabase.pl
>     <http://load_seqdatabase.pl> with my options and I get several
>     warnings and the script halts:
>
>
>     --------------------- WARNING ---------------------
>     MSG: SimpleValueAdaptor::add_assoc: unexpected failure of
>     statement execution: Le champ 'term_id' ne peut Ûtre vide (null)
>             name: INSERT ASSOC [2]
>     Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
>             values: FK[Bio::SeqFeature::Generic]:8,
>     FK[Bio::Annotation::SimpleValue]:, rank:"1", value:"GI:2924601"
>
>
>     --------------------- WARNING ---------------------
>     MSG: SimpleValueAdaptor::add_assoc: unexpected failure of
>     statement execution: Le champ 'term_id' ne peut Ûtre vide (null)
>             name: INSERT ASSOC [2]
>     Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
>             values: FK[Bio::SeqFeature::Generic]:8,
>     FK[Bio::Annotation::SimpleValue]:, value:"hepatocyte growth factor
>     activator inhibitor", rank:"1"
>
>
>     --------------------- WARNING ---------------------
>     MSG: SimpleValueAdaptor::add_assoc: unexpected failure of
>     statement execution: Le champ 'term_id' ne peut Ûtre vide (null)
>             name: INSERT ASSOC [2]
>     Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
>             values: FK[Bio::SeqFeature::Generic]:10,
>     FK[Bio::Annotation::SimpleValue]:, value:"placenta", rank:"1"
>
>
>     --------------------- WARNING ---------------------
>     MSG: SimpleValueAdaptor::add_assoc: unexpected failure of
>     statement execution: Le champ 'term_id' ne peut Ûtre vide (null)
>             name: INSERT ASSOC [2]
>     Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
>             values: FK[Bio::SeqFeature::Generic]:11,
>     FK[Bio::Annotation::SimpleValue]:, value:"1", rank:"1"
>
>
>     --------------------- WARNING ---------------------
>     MSG: SimpleValueAdaptor::add_assoc: unexpected failure of
>     statement execution: Le champ 'term_id' ne peut Ûtre vide (null)
>             name: INSERT ASSOC [2]
>     Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
>             values: FK[Bio::SeqFeature::Generic]:11,
>     FK[Bio::Annotation::SimpleValue]:, rank:"1", value:"GI:3090432"
>
>
>     --------------------- WARNING ---------------------
>     MSG: SimpleValueAdaptor::add_assoc: unexpected failure of
>     statement execution: Le champ 'term_id' ne peut Ûtre vide (null)
>             name: INSERT ASSOC [2]
>     Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
>             values: FK[Bio::SeqFeature::Generic]:11,
>     FK[Bio::Annotation::SimpleValue]:, rank:"1", value:"DCRB"
>
>
>     --------------------- WARNING ---------------------
>     MSG: SimpleValueAdaptor::add_assoc: unexpected failure of
>     statement execution: Le champ 'term_id' ne peut Ûtre vide (null)
>             name: INSERT ASSOC [2]
>     Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
>             values: FK[Bio::SeqFeature::Generic]:11,
>     FK[Bio::Annotation::SimpleValue]:, value:"BAA25877.1", rank:"1"
>
>
>     --------------------- WARNING ---------------------
>     MSG: SimpleValueAdaptor::add_assoc: unexpected failure of
>     statement execution: Le champ 'term_id' ne peut Ûtre vide (null)
>             name: INSERT ASSOC [2]
>     Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
>             values: FK[Bio::SeqFeature::Generic]:11,
>     FK[Bio::Annotation::SimpleValue]:,
>     value:"MSLIILTRDDEPRIFTPDSDAASPALHSTSPLPDPASASPLHREEKILPKVCNIVSCLSFSLPASPTDS
>     GLASPTIITREGQQFWAKCLIWKYQLYLHGLHKKSDGRRDKQISASPST", rank:"1"
>     ---------------------------------------------------
>     Could not store AB000114:
>     ------------- EXCEPTION -------------
>     MSG: Unique key query in Bio::DB::BioSQL::SimpleValueAdaptor
>     returned 2 rows instead of 1. Query was
>     [tagname="keyword",ontology="7"]
>     STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>     C:/strawberry/perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:978
>     STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>     C:/strawberry/perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:873
>     STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
>     C:/strawberry/perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:195
>
>
>     STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
>     C:/strawberry/perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264
>     STACK Bio::DB::Persistent::PersistentObject::store
>     C:/strawberry/perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:284
>     STACK Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children
>     C:/strawberry/perl/site/lib/Bio\DB\BioSQL\AnnotationCollectionAdaptor.pm:230
>     STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
>     C:/strawberry/perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:227
>
>
>     STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
>     C:/strawberry/perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264
>     STACK Bio::DB::Persistent::PersistentObject::store
>     C:/strawberry/perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:284
>     STACK Bio::DB::BioSQL::SeqAdaptor::store_children
>     C:/strawberry/perl/site/lib/Bio\DB\BioSQL\SeqAdaptor.pm:237
>     STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
>     C:/strawberry/perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:227
>
>
>     STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
>     C:/strawberry/perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264
>     STACK Bio::DB::Persistent::PersistentObject::store
>     C:/strawberry/perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:284
>     STACK (eval) load_seqdatabase.pl:630 <http://load_seqdatabase.pl:630>
>     STACK toplevel load_seqdatabase.pl:612
>     <http://load_seqdatabase.pl:612>
>     -------------------------------------
>
>      at load_seqdatabase.pl <http://load_seqdatabase.pl> line 643,
>     <GEN0> line 249.
>
>
>     Then when I look at the records in the database, I have a total of
>     102 records in the database.
>
>     I tested something else... I emptied all tables again (truncating
>     bioentry, reference and ontology first, then all the other tables)
>     and came back to 0 record in the database. Then I launched the
>     script again... and this is very strange as I do not get the same
>     number of records each time I try this (sometimes 70, or 99, or
>     many other number of records so far I've tested). The process
>     doesn't seem to be stable.
>
>     During the installation of BioPerl (1.6.923) and BioPerl-DB
>     (1.006900), I got a lot of warnings. I had to force installation
>     to complete but as I mentioned in my previous message, I'm not
>     sure about what I was really doing.
>     When I test (cpan utility) for BioPerl, I see there's a lot of
>     missing modules, in particular:
>
>     Algorithm::Munkres is not installed
>     Array::Compare is not installed
>     Convert::Binary::C is not installed
>     Error is not installed
>     Graph is not installed
>     GraphViz is not installed
>     HTML::TableExtract is not installed
>     PostScript::TextBlock is not installed
>     SVG is not installed
>     SVG::Graph is not installed
>     Set::Scalar is not installed
>     Spreadsheet::ParseExcel is not installed
>     XML::Parser::PerlSAX is not installed
>     XML::SAX::Writer is not installed
>     XML::Twig is not installed
>     XML::Writer is not installed
>
>     and another warning for "Bio::ASN1::EntrezGene is not installed"
>
>     Do I need all? None? I accepted all default options proposed for
>     build. Here is the test summary report for BioPerl-1.6.932:
>
>     Test Summary Report
>     -------------------
>     t/Assembly/core.t                    (Wstat: 6400 Tests: 246
>     Failed: 0)
>       Non-zero exit status: 25
>       Parse errors: Bad plan.  You planned 890 tests but ran 246.
>     t/Root/RootIO.t                      (Wstat: 6400 Tests: 45 Failed: 1)
>       Failed test:  13
>       Non-zero exit status: 25
>       Parse errors: Bad plan.  You planned 77 tests but ran 45.
>     t/SearchIO/hmmer.t                   (Wstat: 0 Tests: 298 Failed: 1)
>       Failed test:  298
>       Parse errors: Bad plan.  You planned 327 tests but ran 298.
>     t/Tools/Run/WBCommandExts.t          (Wstat: 256 Tests: 25 Failed: 1)
>       Failed test:  25
>       Non-zero exit status: 1
>     Files=337, Tests=18515, 836 wallclock secs ( 6.36 usr +  2.28 sys
>     = 8.64 CPU)
>     Result: FAIL
>     Failed 4/337 test programs. 3/18515 subtests failed.
>       CJFIELDS/BioPerl-1.6.923.tar.gz
>       C:\strawberry\perl\bin\perl.exe ./Build test -- NOT OK
>     //hint// to see the cpan-testers results for installing this
>     module, try:
>       reports CJFIELDS/BioPerl-1.6.923.tar.gz
>     Stopping: 'test' failed for 'BioPerl'.
>     Failed during this command:
>      CJFIELDS/BioPerl-1.6.923.tar.gz              : make_test NO
>
>     For BioPerl-DB, I just got a DBD::Oracle proposal, but I just use
>     mysql so I think it's safe to skip it?
>     Well, for the tests, I get a huge list and I cannot put all
>     here... Here are just the "last" lines, but there are many
>     "Subroutine division redefined at" statements (meanly in
>     species.pm <http://species.pm>)...
>
>     Test Summary Report
>     -------------------
>     t\02species.t   (Wstat: 512 Tests: 25 Failed: 1)
>       Failed test:  25
>       Non-zero exit status: 2
>       Parse errors: Bad plan.  You planned 67 tests but ran 25.
>     t\03simpleseq.t (Wstat: 65280 Tests: 48 Failed: 0)
>       Non-zero exit status: 255
>       Parse errors: Bad plan.  You planned 70 tests but ran 48.
>     t\04swiss.t     (Wstat: 65280 Tests: 8 Failed: 0)
>       Non-zero exit status: 255
>       Parse errors: Bad plan.  You planned 55 tests but ran 8.
>     t\05seqfeature.t (Wstat: 65280 Tests: 6 Failed: 0)
>       Non-zero exit status: 255
>       Parse errors: Bad plan.  You planned 52 tests but ran 6.
>     t\10ensembl.t   (Wstat: 512 Tests: 5 Failed: 0)
>       Non-zero exit status: 2
>       Parse errors: Bad plan.  You planned 18 tests but ran 5.
>     t\11locuslink.t (Wstat: 1792 Tests: 79 Failed: 7)
>       Failed tests:  69-75
>       Non-zero exit status: 7
>       Parse errors: Bad plan.  You planned 113 tests but ran 79.
>     t\12ontology.t  (Wstat: 512 Tests: 5 Failed: 1)
>       Failed test:  5
>       Non-zero exit status: 2
>       Parse errors: Bad plan.  You planned 740 tests but ran 5.
>     t\13remove.t    (Wstat: 65280 Tests: 9 Failed: 0)
>       Non-zero exit status: 255
>       Parse errors: Bad plan.  You planned 61 tests but ran 9.
>     t\15cluster.t   (Wstat: 65280 Tests: 7 Failed: 0)
>       Non-zero exit status: 255
>       Parse errors: Bad plan.  You planned 162 tests but ran 7.
>     Files=16, Tests=335, 44 wallclock secs ( 0.30 usr +  0.14 sys =
>     0.44 CPU)
>     Result: FAIL
>     Failed 9/16 test programs. 9/335 subtests failed.
>       CJFIELDS/BioPerl-DB-1.006900.tar.gz
>       C:\strawberry\perl\bin\perl.exe ./Build test -- NOT OK
>     //hint// to see the cpan-testers results for installing this
>     module, try:
>       reports CJFIELDS/BioPerl-DB-1.006900.tar.gz
>     Stopping: 'test' failed for
>     'C/CJ/CJFIELDS/BioPerl-DB-1.006900.tar.gz'.
>     Failed during this command:
>      CJFIELDS/BioPerl-DB-1.006900.tar.gz          : make_test NO
>
>     At the end of the test process, I see my biosql_hs db was accessed
>     as I find a few new records in some tables.
>
>     Well, all is here I hope. I'm starting to get in the install
>     process on my Ubuntu virtual box to verify I could make it work
>     better with Linux perhaps. Perhaps I'll also install the modules
>     proposed, never know...
>     But if you find anything that could explain all that, I'm really
>     interested !
>
>     Thanks for reading and help !
>
>     Kind regards
>
>     Olivier
>
>     Le 26/03/2014 00:09, Hilmar Lapp a écrit :
>
>         Are you sure that the database was empty that you were trying
>         to load into?
>
>         The error you're seeing means that some object wasn't found in
>         the database when searching for it by (compound) unique key,
>         but then inserting the object raised an exception, presumably
>         due to unique key failure. Sometimes this can happen when a
>         sequence's component objects are manipulated by a script. But
>         that doesn't seem to be what you are doing, so it's not clear
>         to me what might be going on.
>
>         Did you run the bioperl-db tests, and if so, did they pass?
>
>           -hilmar
>
>
>         On Mon, Mar 24, 2014 at 8:51 AM, Olivier BUHARD
>         <Olivier.Buhard <at> inserm.fr <mailto:Olivier.Buhard <at> inserm.fr>
>         <mailto:Olivier.Buhard <at> inserm.fr
>         <mailto:Olivier.Buhard <at> inserm.fr>>> wrote:
>
>             Hi,
>
>             thank you a lot Christopher, Francisco and Hilmar for your
>         great help!
>
>             I followed all your propositions. Changed to Strawberry Perl
>             (latest version, and I uninstalled Activeperl before) and
>         I can
>             now have a connection to the local mysql server on my
>         computer.
>             I look a bit closer in the files generated during the build
>             process (in cpan utility) in the meanwhile and found as you
>             mention below, a problem with the DBD::mysql that didn't
>         take into
>             account the connection parameters I pass through the
>         Makefile.PL
>             script. Looking further into the code, I saw the script
>         asked for
>             both user AND password... and I didn't have a password for
>         that
>             specific user accessing my biosql db... there was a function
>             called "win32_config" or something like this that then
>         generated
>             the configuration for the tests with a default user 'ODBC'
>         I don't
>             use.
>             Well, this is just for the "little story".
>             Now I checked my DBI and mysql DBD, they work fine. I can
>         retrieve
>             data from another mysql database I use frequently.
>
>             Then I installed BioPerl (1.6.923) and BioPerl-DB
>         (1.006900). I
>             had to force install for both because I got many
>         exceptions, and
>             particularly one in Bio::Root::IO i'm a bit worried about,
>         I feel
>             it's an important piece of the module.
>             Once I finished install, I tried load_seqdatabase.pl
>         <http://load_seqdatabase.pl>
>             <http://load_seqdatabase.pl> on a truncated version of the
>         same
>
>             gbpri1.seq from NCBI FTP. But again it doesn't work, but for a
>             different reason than before I think. I get a connection to my
>             biosql database, but there is some glitch, I can't find
>         out what
>             happens.
>             The script threw me a lot of warning messages, saying
>         "failed to
>             insert or to be found by unique key".
>
>             As I forced the installation of BioPerl and BioPerl-DB, is
>         there a
>             chance I missed some critical message? It seems the
>         problem is in
>             the BioPerl-DB module but not related to the connection
>         (when I
>             enter a wrong user, I get a denied access message, so it's
>         OK for
>             the connection apparently).
>             I'll try on a Linux install soon to verify. But if you
>         have any
>             idea in the meanwhile, I'll appreciate a lot!
>
>             Below is the output from the load_seqdatabase script I get:
>
>             Many thanks for your (really appreciated) help!
>
>             Best regards.
>
>             Olivier
>             -----------------------
>             C:\Perl Bio Scripts>perl load_seqdatabase.pl
>         <http://load_seqdatabase.pl>
>             <http://load_seqdatabase.pl> --dbname=biosql_hs
>
>             --dbuser=biodb_user gbTest.seq
>
>             Loading gbTest.seq ...
>             Subroutine new redefined at
>             C:/strawberry/perl/site/lib/Bio\Species.pm line 120,
>          <GEN0> line 98.
>             Subroutine classification redefined at
>             C:/strawberry/perl/site/lib/Bio\Species.pm line 176,
>         <GEN0> line 98.
>             Subroutine species redefined at
>             C:/strawberry/perl/site/lib/Bio\Species.pm line272, <GEN0>
>         line 98.
>             Subroutine genus redefined at
>             C:/strawberry/perl/site/lib/Bio\Species.pm line 377,
>         <GEN0> line 98.
>             Subroutine sub_species redefined at
>             C:/strawberry/perl/site/lib/Bio\Species.pm line 407,
>         <GEN0> line 98.
>             Subroutine variant redefined at
>             C:/strawberry/perl/site/lib/Bio\Species.pm line455, <GEN0>
>         line 98.
>             Subroutine binomial redefined at
>             C:/strawberry/perl/site/lib/Bio\Species.pm line 490,
>         <GEN0> line 98.
>             Subroutine validate_species_name redefined at
>             C:/strawberry/perl/site/lib/Bio\Species.pm line 530,
>         <GEN0> line 98.
>             Subroutine validate_name redefined at
>             C:/strawberry/perl/site/lib/Bio\Species.pm line 539,
>         <GEN0> line 98.
>
>             .../...
>
>             Subroutine remove_Descendant redefined at
>             C:/strawberry/perl/site/lib/Bio\Species.pm line 604,
>         <GEN0> line 98.
>             Subroutine name redefined at
>             C:/strawberry/perl/site/lib/Bio\Species.pm line 606,
>         <GEN0> line 98.
>             Subroutine taxon redefined at
>             C:/strawberry/perl/site/lib/Bio\Species.pm line 619,
>         <GEN0> line 98.
>             Subroutine tree redefined at
>             C:/strawberry/perl/site/lib/Bio\Species.pm line 639,
>         <GEN0> line 98.
>             Subroutine DESTROY redefined at
>             C:/strawberry/perl/site/lib/Bio\Species.pm line649, <GEN0>
>         line 98.
>
>             --------------------- WARNING ---------------------
>             MSG: SimpleValueAdaptor::add_assoc: unexpected failure of
>             statement execution: Le champ 'term_id' ne peut Ûtre vide
>         (null)
>                     name: INSERT ASSOC [2]
>             Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
>                     values: FK[Bio::SeqFeature::Generic]:3,
>             FK[Bio::Annotation::SimpleValue]:, value:"mRNA", rank:"1"
>             ---------------------------------------------------
>
>             --------------------- WARNING ---------------------
>             MSG: SimpleValueAdaptor::add_assoc: unexpected failure of
>             statement execution: Le champ 'term_id' ne peut Ûtre vide
>         (null)
>                     name: INSERT ASSOC [2]
>             Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
>                     values: FK[Bio::SeqFeature::Generic]:3,
>             FK[Bio::Annotation::SimpleValue]:, rank:"1", value:"Homo
>         sapiens"
>             ---------------------------------------------------
>
>             --------------------- WARNING ---------------------
>             MSG: SimpleValueAdaptor::add_assoc: unexpected failure of
>             statement execution: Le champ 'term_id' ne peut Ûtre vide
>         (null)
>                     name: INSERT ASSOC [2]
>             Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
>                     values: FK[Bio::SeqFeature::Generic]:4,
>             FK[Bio::Annotation::SimpleValue]:, value:"hepatocyte
>         growth factor
>             activator inhibitor", rank:"1"
>             ---------------------------------------------------
>
>             --------------------- WARNING ---------------------
>             MSG: SimpleValueAdaptor::add_assoc: unexpected failure of
>             statement execution: Le champ 'term_id' ne peut Ûtre vide
>         (null)
>                     name: INSERT ASSOC [2]
>             Bio::SeqFeature::Generic;Bio::Annotation::SimpleValue
>                     values: FK[Bio::SeqFeature::Generic]:4,
>             FK[Bio::Annotation::SimpleValue]:, value:"BAA25014.1",
>         rank:"1"
>             ---------------------------------------------------
>             Could not store AB000099:
>             ------------- EXCEPTION -------------
>             MSG: create: object (Bio::Species) failed to insert or to
>         be found
>             by unique key
>             STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
>            
>         C:/strawberry/perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:219
>             STACK Bio::DB::Persistent::PersistentObject::create
>            
>         C:/strawberry/perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:257
>             STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
>            
>         C:/strawberry/perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:182
>             STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
>            
>         C:/strawberry/perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:264
>             STACK Bio::DB::Persistent::PersistentObject::store
>            
>         C:/strawberry/perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:284
>             STACK (eval) load_seqdatabase.pl:630
>         <http://load_seqdatabase.pl:630> <http://load_seqdatabase.pl:630>
>             STACK toplevel load_seqdatabase.pl:612
>         <http://load_seqdatabase.pl:612>
>             <http://load_seqdatabase.pl:612>
>             -------------------------------------
>
>
>              at load_seqdatabase.pl <http://load_seqdatabase.pl>
>         <http://load_seqdatabase.pl> line 643,
>
>             <GEN0> line 162.
>
>
>
>
>             Le 21/03/2014 05:59, Fields, Christopher J a écrit :
>
>                 Agree with Francisco, Strawberry Perl is definitely
>         the way to
>                 go.  You can do it with ActivePerl but IIRC the PPM
>         installs
>                 were always a pain.
>
>                 chris
>
>                 On Mar 20, 2014, at 10:54 PM, Francisco J. Ossandón
>                 <fossandonc <at> hotmail.com
>         <mailto:fossandonc <at> hotmail.com> <mailto:fossandonc <at> hotmail.com
>         <mailto:fossandonc <at> hotmail.com>>> wrote:
>
>                     Hi Olivier,
>                     Currently there is no PPM package from the latest
>         version,
>                     the last one is
>                     like 4 years old, so is better to download the latest
>                     version from CPAN
>                     (1.6.923).
>                     I have one recommendation though... unless you are
>         very
>                     attached to
>                     ActivePerl, uninstall it and install Strawberry
>         Perl instead
>                     (http://strawberryperl.com/).
>
>                     When I started to learn Bioperl several years ago
>         I used
>                     ActivePerl too, but
>                     it always gave me trouble installing new modules from
>                     CPAN. I switched to
>                     Strawberry a few years ago and is much better
>         because it
>                     includes by default
>                     additional libraries and compiling tools (gcc, mingw,
>                     dmake, etc) that makes
>                     easier the installation of CPAN modules (including
>         some
>                     Bioperl
>                     dependencies)... Since the installation
>         instructions at
>                     the wiki only
>                     considered ActivePerl, I updated the wiki a few
>         days ago
>                     to include
>                     Strawberry Perl as an additional option
>                     (http://www.bioperl.org/wiki/Special:RecentChanges).
>
>                     By the way... something odd among the errors you are
>                     getting is that it says
>                     that " perl514.dll cannot be found", but if you
>         installed
>                     5.18 you should
>                     have perl518.dll instead... did you install 5.18 above
>                     5.14?? Because I can
>                     tell that overwriting it can produce obscure and
>                     mysterious bugs, is better
>                     to uninstall the old one first, then delete the whole
>                     folder, and then make
>                     a clean install of the new one.
>
>                     Cheers and good luck,
>
>                     Francisco J. Ossandon
>
>                     -----Mensaje original-----
>                     De: bioperl-l-bounces <at> lists.open-bio.org
>         <mailto:bioperl-l-bounces <at> lists.open-bio.org>
>                     <mailto:bioperl-l-bounces <at> lists.open-bio.org
>         <mailto:bioperl-l-bounces <at> lists.open-bio.org>>
>                     [mailto:bioperl-l-bounces <at> lists.open-bio.org
>         <mailto:bioperl-l-bounces <at> lists.open-bio.org>
>
>                     <mailto:bioperl-l-bounces <at> lists.open-bio.org
>         <mailto:bioperl-l-bounces <at> lists.open-bio.org>>] En nombre
>                     de Hilmar Lapp
>                     Enviado el: jueves, 20 de marzo de 2014 20:49
>                     Para: Olivier BUHARD
>                     CC: BioPerl List
>                     Asunto: Re: [Bioperl-l] New to BioPerl ... part II
>
>                     I think the exception message appears due to the
>         actual
>                     problem you're
>                     already describing. Bioperl-db will catch the
>         failure and
>                     then print the
>                     error message. Since it doesn't seem to say
>         anything about
>                     failing to
>                     connect to the database, it's either failing before or
>                     past that point for
>                     an unexpected reason. My suspicion is that it fails to
>                     load the DBD driver
>                     for Perl DBI.
>
>                     You can test that by writing a small script (not using
>                     Bioperl or
>                     Bioperl-DB) that simply opens a connection to the
>                     database. If that fails,
>                     that's where the problem is.
>
>                     You can also try that with Bioperl-db:
>
>                       $conn =
>         $dbadp->dbcontext()->dbi()->new_connection();
>
>                     This should give you an open DBI-compliant connection.
>
>                     If that part works, then the problem is somewhere
>         with the
>                     dynamic
>                     auto-loading code.
>
>                     -hilmar
>
>
>
>                     On Wed, Mar 19, 2014 at 6:46 PM, Olivier BUHARD
>                     <Olivier.Buhard <at> inserm.fr
>         <mailto:Olivier.Buhard <at> inserm.fr>
>                     <mailto:Olivier.Buhard <at> inserm.fr
>         <mailto:Olivier.Buhard <at> inserm.fr>>>wrote:
>
>
>                         Hi,
>
>                         thank you all for your answers. I had the (wrong)
>                         notion that windows
>                         did ignore the shebang...
>
>                         I am using Bioperl 1.6.1... I'll try to install
>                         1.6.923 but I can't
>                         find it with ActivePerl ppm (I switched to
>         5.18), so
>                         I'll have to try
>                         with command line ppm. I'm running windows XP...
>                         perhaps also have to
>                         try with Linux.
>
>                         I'm getting in the doc and tutos I can find about
>                         Bioperl-db and I'm
>                         beginning to understand how it deals with
>         parsing and
>                         organizing the data.
>                         However, my first attempts to load sequences in my
>                         BioSQL db are
>                         unsuccessful. From the gbpri1.seq I downloaded
>         from
>                         NCBI FTP,
>         load_seqdatabase.pl <http://load_seqdatabase.pl>
>         <http://load_seqdatabase.pl>
>
>                         crashes at the moment it tries to INSERT in the
>                         db, telling me perl514.dll cannot be found, and
>                         sending a bunch of
>                         error messages in a last breath:
>
>                         C:\tmp>perl load_seqdatabase.pl
>         <http://load_seqdatabase.pl>
>                         <http://load_seqdatabase.pl> -dbname biosql_hs
>         -dbuser
>
>                         biodb_user
>                         -dbpass ******** gbpri1.seq Loading gbpri1.seq ...
>                         UNIVERSAL->import is deprecated and will be
>         removed in
>                         a future perl
>                         UNIVERSAL->at
>                         C:/Perl/site/lib/Bio/Tree/TreeFunctionsI.pm
>         line 94.
>                         UNIVERSAL->import is deprecated and will be
>         removed in
>                         a future perl
>                         UNIVERSAL->at
>                         C:/Perl/site/lib/Bio\Tree\TreeFunctionsI.pm
>         line 94.
>
>                         ------------- EXCEPTION -------------
>                         MSG: failed to open connection:
>                         STACK Bio::DB::DBI::base::new_connection
>                         C:/Perl/site/lib/Bio/DB/DBI/ba
>         se.pm:267 <http://se.pm:267> <http://se.pm:267>
>
>                         STACK Bio::DB::DBI::base::get_connection
>                         C:/Perl/site/lib/Bio/DB/DBI/ba
>         se.pm:227 <http://se.pm:227> <http://se.pm:227>
>
>                         STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbh
>                        
>         C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1498
>                         STACK
>         Bio::DB::BioSQL::BasePersistenceAdaptor::rollback
>                        
>         C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1417
>                         STACK toplevel load_seqdatabase.pl:636
>         <http://load_seqdatabase.pl:636>
>                         <http://load_seqdatabase.pl:636>
>
>                         -------------------------------------
>
>                         I think I'm doing something wrong, but I can't
>         find
>                         what. The mySQL
>                         server (version 4.1.9) is on, I've installed
>         the DBI
>                         and DBD::mySQL. I
>                         checked the user for its privileges and
>         password, so
>                         what can be wrong?
>
>                         I've tried writing a shorter script to get in the
>                         command that breaks
>                         the process (below) and I found it was when it
>         tries
>                         to ->create():
>
>                         #!perl
>
>                         use strict;
>                         use Bio::DB::BioDB;
>                         use Bio::SeqIO;
>
>                         my $seq_file = shift or die("GB_crawler.pl -
>         Usage : perl
>                         GB_crawler.pl <SEQ_FILE>\n\n");
>
>                         my $dbadp = Bio::DB::BioDB->new(  -database  =>
>                         'biosql',
>         -host  => 'localhost',
>         -user => 'biodb_user',
>         -pass  =>
>                         'THE_PASSWORD_HERE',
>         -dbname =>
>                         'biosql_hs',
>         -driver => 'mysql'
>                         );
>                         $dbadp->verbose(1);
>
>                         my $seqio_obj = Bio::SeqIO->new(-file =>
>         "<$seq_file",
>                         -format =>
>                         'genbank' ); while (my $seq_obj =
>         $seqio_obj->next_seq()){
>                             print $seq_obj->display_id(),"\n";
>                             my $species = $seq_obj->species();
>                             my $seq_spec = $species->binomial();
>                             if ($seq_spec eq 'Homo sapiens') {    #
>         I'm just
>                         interested in Hs seq
>                                 my $p_seq =
>         $dbadp->create_persistent($seq_obj);
>                                 $p_seq->create();
>                             }
>                         }
>
>                         The output is: (I can't put all here, it' too
>         long...)
>
>                         C:\tmp>perl GB_crawler.pl gbpri1.seq
>
>                         UNIVERSAL->import is deprecated and will be
>         removed in
>                         a future perl
>                         UNIVERSAL->at
>                         C:/Perl/site/lib/Bio/Tree/TreeFunctionsI.pm
>         line 94.
>                         AB000095
>                         attempting to load adaptor class for
>         Bio::Seq::RichSeq
>                                 attempting to load module
>                         Bio::DB::BioSQL::RichSeqAdaptor
>                         attempting to load adaptor class for Bio::Seq
>                                 attempting to load module
>                         Bio::DB::BioSQL::SeqAdaptor
>                         instantiating adaptor class
>         Bio::DB::BioSQL::SeqAdaptor
>
>                         .../...
>
>                         attempting to load adaptor class for
>                         Bio::Tree::TreeFunctionsI
>                                 attempting to load module
>                         Bio::DB::BioSQL::TreeFunctionsIAdaptor
>                                 attempting to load module
>                         Bio::DB::BioSQL::TreeFunctionsAdaptor
>                         UNIVERSAL->import is deprecated and will be
>         removed in
>                         a future perl
>                         UNIVERSAL->at
>                         C:/Perl/site/lib/Bio\Tree\TreeFunctionsI.pm
>         line 94.
>                         no adaptor found for class Bio::Tree::Tree no
>         adaptor
>                         found for class
>                         Bio::Annotation::TypeManager no adaptor found
>         for class
>                         Bio::DB::Taxonomy::list no adaptor found for class
>                         Bio::Tree::Tree
>                         attempting to load adaptor class for BioNamespace
>                                 attempting to load module
>                         Bio::DB::BioSQL::BioNamespaceAdaptor
>                         instantiating adaptor class
>                         Bio::DB::BioSQL::BioNamespaceAdaptor
>                         no adaptor found for class
>                         Bio::Annotation::TypeManager no adaptor
>                         found for class Bio::DB::Taxonomy::list no adaptor
>                         found for class
>                         Bio::Tree::Tree attempting to load driver for
>         adaptor
>                         class
>                         Bio::DB::BioSQL::
>                         BioNamespaceAdaptor
>
>                         attempting to load driver for adaptor class
>                         Bio::DB::BioSQL::
>                         BasePersistenceAdaptor
>                         Using
>                        
>         Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver
>                         as driver
>                         peer for Bio::DB::BioSQL::BioNamespaceAdaptor
>
>                         ------------- EXCEPTION -------------
>                         MSG: failed to open connection:
>                         STACK Bio::DB::DBI::base::new_connection
>                         C:/Perl/site/lib/Bio/DB/DBI/ba
>         se.pm:267 <http://se.pm:267> <http://se.pm:267>
>
>
>                         STACK Bio::DB::DBI::base::get_connection
>                         C:/Perl/site/lib/Bio/DB/DBI/ba
>         se.pm:227 <http://se.pm:227> <http://se.pm:227>
>
>
>                         STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbh
>                        
>         C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1498
>                         STACK Bio::DB::BioSQL::BaseDriver::insert_object
>                         C:/Perl/site/lib/Bio/DB/
>                         BioSQL/BaseDriver.pm:970
>                         STACK
>         Bio::DB::BioSQL::BasePersistenceAdaptor::create
>                        
>         C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:212
>                         STACK
>         Bio::DB::Persistent::PersistentObject::create
>                        
>         C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:257
>                         STACK
>         Bio::DB::BioSQL::BasePersistenceAdaptor::create
>                        
>         C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:182
>                         STACK
>         Bio::DB::Persistent::PersistentObject::create
>                        
>         C:/Perl/site/lib/Bio/DB/Persistent/PersistentObject.pm:257
>                         STACK toplevel GB_crawler.pl:52
>                         -------------------------------------
>
>                         Again, the script halts asking for
>         Perl514.dll, then
>                         the EXCEPTION MSG
>                         appears...
>                         Is there a chance ActivePerl 5.18 couldn't
>         work with
>                         Bioperl-DB (I
>                         have
>                         1.006000 version)?
>
>                         Thanks for any answer !
>
>                         Best regards
>
>                         Olivier
>
>
>             --
>             --------------------
>
>             BUHARD Olivier
>
>             "Instabilité de microsatellites et cancer"
>             Centre de Recherche Saint Antoine
>             équipe 11/INSERM UMRS 938
>             Bâtiment Kourilsky,
>             Hôpital Saint Antoine
>             34 rue Crozatier
>             75012 PARIS
>
>
>
>             _______________________________________________
>             Bioperl-l mailing list
>         Bioperl-l <at> lists.open-bio.org
>         <mailto:Bioperl-l <at> lists.open-bio.org>
>         <mailto:Bioperl-l <at> lists.open-bio.org
>         <mailto:Bioperl-l <at> lists.open-bio.org>>
>         http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
>         -- 
>         Hilmar Lapp -:- lappland.io <http://lappland.io>
>         <http://lappland.io>
>
>
>     -- 
>
>     --------------------
>
>     BUHARD Olivier
>
>     "Instabilité de microsatellites et cancer"
>     Centre de Recherche Saint Antoine
>     équipe 11/INSERM UMRS 938
>     Bâtiment Kourilsky,
>     Hôpital Saint Antoine
>     34 rue Crozatier
>     75012 PARIS
>
>     --------------------
>     Tél : 01 49 28 66 61
>     --------------------
>
>
>
>     _______________________________________________
>     Bioperl-l mailing list
>     Bioperl-l <at> lists.open-bio.org <mailto:Bioperl-l <at> lists.open-bio.org>
>     http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> -- 
> Hilmar Lapp -:- lappland.io <http://lappland.io>
>

--

-- 

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

BUHARD Olivier

"Instabilité de microsatellites et cancer"
Centre de Recherche Saint Antoine
équipe 11/INSERM UMRS 938
Bâtiment Kourilsky,
Hôpital Saint Antoine
34 rue Crozatier
75012 PARIS

--------------------
Tél : 01 49 28 66 61
--------------------

Gmane