[Bioperl-l] New to BioPerl ... part II
Hilmar Lapp
hlapp at drycafe.net
Mon Apr 28 13:06:33 UTC 2014
Hi Olivier,
That's great to hear it works on Ubuntu! I wish I had the time figuring out
what the problems are on Windows, but I'm afraid I don't.
-hilmar
On Fri, Apr 25, 2014 at 10:01 AM, Olivier BUHARD
<Olivier.Buhard at inserm.fr>wrote:
> Hi Francisco and Hilmar,
>
> I forgot to give some news... Finally, it works fine on my Ubuntu (12.04)
> virtual box. I successfully installed all the stuff I need (even with a lot
> of warnings and errors) and ran the load_seqdatabase.pl with the
> trunctated version of gbpri1.seq I used to work with for those tests. I now
> have to populate my bioSQL db with GenBank data for human gene sequences. I
> think I will keep it all working with Ubuntu as I don't have time to deal
> with all the work it require starting again under Windows...
>
> Once I'll be done with the database, I will have to crawl in it to find
> microsatellite sequences and fiter then regarding their features and
> annotations (exon, intron, UTRs, etc etc...). If somebody knows it already
> been coded in Perl, I'm very interested!
>
> Thanks again for the help you brougth.
>
> Best regards
>
> Olivier
>
>
> Le 27/03/2014 22:25, Francisco J. Ossandón a écrit :
>
>> Hi Olivier,
>> After the last release of BioPerl, I started to work to resolve all those
>> issues that only appear in Windows (the inplace edit in Bio::Root::IO, the
>> "cannot unlink file" errors, the use of 'cat' linux comand), and now all
>> tests pass in my Windows system (if there is any error in the latest code
>> let me know). Those fixes will be present in the next release of BioPerl,
>> BUT you can download the current developer version before the next
>> official
>> release, if you go to the GitHub repository corresponding branch
>> (https://github.com/bioperl/bioperl-live/tree/v1.6.x) and press the
>> Download
>> ZIP button. By the way, you can safely ignore some messages that are
>> warnings and not errors (the BioDBGFF.t message and the "subroutine xxxx
>> redefined" messages).
>>
>> For BioPerl-DB, the last release was 3 years ago and I have not checked it
>> in Windows yet, so it could have unresolved bugs. My recent experience
>> have
>> shown me that the difference in the characters used as line-ending between
>> linux (1 char) and windows (2 chars), is a common source of bugs. =/
>>
>> Cheers,
>>
>> Francisco J. Ossandon
>>
>>
>> -----Mensaje original-----
>> De: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Olivier BUHARD
>> Enviado el: jueves, 27 de marzo de 2014 9:25
>> Para: BioPerl List
>>
>> Asunto: Re: [Bioperl-l] 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/B
>> asePersistenceAdaptor.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/B
>> asePersistenceAdaptor.pm:873
>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>> C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\
>> blib\lib/Bio/DB/BioSQL/B
>> asePersistenceAdaptor.pm:195
>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>> C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\
>> blib\lib/Bio/DB/BioSQL/B
>> asePersistenceAdaptor.pm:264
>> STACK: Bio::DB::Persistent::PersistentObject::store
>> C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\
>> blib\lib/Bio/DB/Persiste
>> nt/PersistentObject.pm:284
>> STACK: Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children
>> C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\
>> blib\lib/Bio\DB\BioSQL\A
>> nnotationCollectionAdaptor.pm:230
>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>> C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\
>> blib\lib/Bio/DB/BioSQL/B
>> asePersistenceAdaptor.pm:227
>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>> C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\
>> blib\lib/Bio/DB/BioSQL/B
>> asePersistenceAdaptor.pm:264
>> STACK: Bio::DB::Persistent::PersistentObject::store
>> C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\
>> blib\lib/Bio/DB/Persiste
>> nt/PersistentObject.pm:284
>> STACK: Bio::DB::BioSQL::SeqAdaptor::store_children
>> C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\
>> blib\lib/Bio\DB\BioSQL\S
>> eqAdaptor.pm:237
>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>> C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\
>> blib\lib/Bio/DB/BioSQL/B
>> asePersistenceAdaptor.pm:227
>> STACK: Bio::DB::Persistent::PersistentObject::create
>> C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\
>> blib\lib/Bio/DB/Persiste
>> nt/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
>> LEQQSIVHIVQRPRRRSHETNASGGDEPQSTSEGSIWESRSLTRVDLSSHTLPVDSVGLA
>> VILDTDSKRDSEAARG
>> PVKP
>> TYNSFFIYCKGPCHKVQPGKLRVQCGTCKQATLTLAQGPSCWDDVLIPNRMSGECQSPDC
>> PGTRAEFFFKCGAHPT
>> SDKD
>> TSVALNLITSNRRSIPCIACTDVRSPVLVFQCNHRHVICLDCFHLYCVTRLNDRQFVHDA
>> QLGYSLPCVAGCPNSL
>> IKEL
>> HHFRILGEEQYTRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEQGQRKVTCEGGNGLGCG
>> FVFCRDCKEAYHEGDC
>> DSLL
>> EPSGATSQAYRVDKRAAEQARWEEASKETIKKTTKPCPRCNVPIEKNGGCMHMKCPQPQC
>> KLEWCWNCGCEWNRAC
>> MGDH
>> 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/B
>> asePersistenceAdaptor.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/B
>> asePersistenceAdaptor.pm:873
>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>> C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\
>> blib\lib/Bio/DB/BioSQL/B
>> asePersistenceAdaptor.pm:195
>> STACK: Bio::DB::Persistent::PersistentObject::create
>> C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\
>> blib\lib/Bio/DB/Persiste
>> nt/PersistentObject.pm:257
>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>> C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\
>> blib\lib/Bio/DB/BioSQL/B
>> asePersistenceAdaptor.pm:182
>> STACK: Bio::DB::Persistent::PersistentObject::create
>> C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\
>> blib\lib/Bio/DB/Persiste
>> nt/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/B
>> asePersistenceAdaptor.pm:219
>> STACK: Bio::DB::Persistent::PersistentObject::create
>> C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\
>> blib\lib/Bio/DB/Persiste
>> nt/PersistentObject.pm:257
>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>> C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\
>> blib\lib/Bio/DB/BioSQL/B
>> asePersistenceAdaptor.pm:182
>> STACK: Bio::DB::Persistent::PersistentObject::create
>> C:\strawberry\cpan\build\BioPerl-DB-1.006900-OUzvBl\
>> blib\lib/Bio/DB/Persiste
>> nt/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:"MSLIILTRDDEPRIFTPDSDAASPALHSTSPLPDPASASPLHREEKILPKVCNIVSCLSF
>> SLPASPTDS
>>
>>> 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
> --------------------
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
--
Hilmar Lapp -:- lappland.io
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