[Bioperl-l] New to BioPerl ... part II
Olivier BUHARD
Olivier.Buhard at inserm.fr
Thu Mar 27 12:24:55 UTC 2014
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
> --------------------
>
>
>
> _______________________________________________
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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
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Tél : 01 49 28 66 61
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