Hilmar Lapp | 26 Mar 15:23 2014
Picon

Re: New to BioPerl ... part II

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>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 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
> STACK toplevel load_seqdatabase.pl:612
> -------------------------------------
>
>  at 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)...
>
> 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>> 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> 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> --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>
>>     STACK toplevel load_seqdatabase.pl:612
>>     <http://load_seqdatabase.pl:612>
>>     -------------------------------------
>>
>>
>>      at 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>> 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>] 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>>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>
>>
>>                 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> -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>
>>
>>                 STACK Bio::DB::DBI::base::get_connection
>>                 C:/Perl/site/lib/Bio/DB/DBI/ba
>>                 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>
>>
>>                 -------------------------------------
>>
>>                 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>
>>
>>
>>                 STACK Bio::DB::DBI::base::get_connection
>>                 C:/Perl/site/lib/Bio/DB/DBI/ba
>>                 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>
>>     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

Gmane