[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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