[Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl
Brian Osborne
brian_osborne at cognia.com
Fri Oct 10 09:27:36 EDT 2003
Cool.
-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Robert Roth
Sent: Friday, October 10, 2003 9:21 AM
To: Brian Osborne; bioperl-l at bioperl.org
Subject: RE: [Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl
Brian,
Thank you for your advice. I got the database set up under cygwin now
and everything seems to work so far. The only thing that caused some trouble
was that I am not able to use 'localhost' as host when running the test for
bioperl-db. Using 127.0.0.1 as described at the link below for the
installation of DBD-mysql also solved these problems. Now
load_seqdatabase.pl seem to work so I guess I'll load the data under cygwin.
/Robert
>
>
> Robert,
>
> > Is there someone else who have a working installation of
> Bioperl/bioperl-db/biosql under windows?
>
> I've not done extensive use or testing of my Mysql database but
> I've set up
> a small one using load_taxonomy.pl followed by
> load_seqdatabase.pl. This was
> a month or so ago. I used Cygwin, the latest bioperl from CVS, latest
> biosql-schema, and the latest bioperl-db, installed in that order. Mysql
> 4.0.13. The only tricky part is getting DBD::Mysql running under Cygwin. I
> was getting a bit frustrated but then I stumbled on this:
>
> http://search.cpan.org/src/JWIED/DBD-mysql-2.1025/INSTALL.html#win
> dows/cygwi
> n
>
>
> Brian O.
>
>
>
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Robert Roth
> Sent: Thursday, October 09, 2003 7:51 AM
> To: bioperl-l at bioperl.org
> Subject: RE: [Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl
>
>
> I started over again and also upgraded to perl 5.8 (from ActiveState). The
> claim in INSTALL.WIN that not all external modules are available from the
> ppm repositories is no longer true.
> Since the the installation of Bioperl with ppm does not give the
> possiblity
> to run the test suite I skipped it and installed Bioperl-1.2.3 with nmake
> instead. The test suite for bioperl ran without any major
> problems. With all
> test that just returned "ok" removed for brevity the output was,
>
> ************************************************************************
> t\Assembly...................DB_File not installed. This means
> the Assembly
> modules are not available. Skipping tests.
> t\Assembly...................ok
> t\DB.........................ok
> 1/78 skipped:
> t\flat.......................DB_File not loaded. This means flat.t test
> cannot
> be executed. Skipping
> t\flat.......................ok
> t\Index......................ok 11/32Can't call method "accession" on an
> undefined value at E:\temp\bioperl-1.2.3\blib\lib/Bio/DB/InMemoryCache.pm
> line 220, <GN7> line 54.
> t\Index......................dubious
> Test returned status 22 (wstat 5632, 0x1600)
> after all the subtests completed successfully
> t\SeqFeatCollection..........DB_File not installed. This means the
> SeqFeatCollection wont work
> t\SeqFeatCollection..........ok
> Failed Test Stat Wstat Total Fail Failed List of Failed
> ------------------------------------------------------------------
> ----------
> ---
> t\Index.t 22 5632 32 0 0.00% ??
> 4 subtests skipped.
> Failed 1/123 test scripts, 99.19% okay. 0/5977 subtests failed, 100.00%
> okay.
> ************************************************************************
>
>
>
> After this I moved on and installed bioperl-db. Running the test
> suite gives
> the lengthy (sorry...) output below. They all (except dbadaptor.t and
> query.t) fail with the same output. Attempting to run load_seqdatabase.pl
> fails with the same output as before.
> The complains about redefined subroutines that I showed in an earlier
> message that I get when running load_seqdatabase.pl is something that is
> known and attributed to a more "sensitive" perl on windows.
> If the problem still seems to be related to the perl setup I
> guess I have to
> build perl also and abandon activestate. Is there someone else who have a
> working installation of Bioperl/bioperl-db/biosql under windows?
> Your help is very much appreciated.
>
> /Robert
>
>
> *************************************************************************
> C:\Perl\bin\perl.exe "-MExtUtils::Command::MM" "-e" "test_harness(0, 'bl
> ib\lib', 'blib\arch')" t\cluster.t t\comment.t t\dbadaptor.t t\dblink.t
> t\ensemb
> l.t t\fuzzy2.t t\genbank.t t\locuslink.t t\ontology.t t\query.t t\remove.t
> t\seq
> feature.t t\simpleseq.t t\species.t t\swiss.t
> t\cluster.......ok 2/160Undefined subroutine
> &Bio::Root::Root::throw called
> at E
> :\temp\bioperl-db\blib\lib/Bio\DB\BioSQL\DBAdaptor.pm line 205,
> <GEN0> line
> 1.
> t\cluster.......dubious
> Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-160
> Failed 158/160 tests, 1.25% okay
> t\comment.......ok 2/11Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> <GEN0>
> line 72.
> t\comment.......dubious
> Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-11
> Failed 9/11 tests, 18.18% okay
> t\dbadaptor.....ok
> t\dblink........ok 2/18Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> <GEN0>
> line 72.
> t\dblink........dubious
> Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-18
> Failed 16/18 tests, 11.11% okay
> t\ensembl.......ok 2/15Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> <GEN0>
> line 1420.
> t\ensembl.......dubious
> Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-15
> Failed 13/15 tests, 13.33% okay
> t\fuzzy2........ok 2/21Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> <GEN0>
> line 64.
> t\fuzzy2........dubious
> Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-21
> Failed 19/21 tests, 9.52% okay
> t\genbank.......ok 2/18Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> <GEN0>
> line 72.
> t\genbank.......dubious
> Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-18
> Failed 16/18 tests, 11.11% okay
> t\locuslink.....ok 3/110Undefined subroutine
> &Bio::Root::Root::throw called
> at E
> :\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> <GEN0
> > line 1.
> t\locuslink.....dubious
> Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 4-110
> Failed 107/110 tests, 2.73% okay
> t\ontology......ok 4/291Undefined subroutine
> &Bio::Root::Root::throw called
> at E
> :\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> <GEN0
> > line 98.
> t\ontology......dubious
> Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 5-291
> Failed 287/291 tests, 1.37% okay
> t\query.........ok
> t\remove........ok 1/59Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> <GEN0>
> line 41.
> (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> at t\
> remove.t line 32, <GEN0> line 41.
> Undefined subroutine &Bio::Root::Root::throw called at
> E:\temp\bioperl-db\blib\l
> ib/Bio\DB\BioSQL\DBAdaptor.pm line 174, <GEN0> line 41.
> t\remove........dubious
> Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 2-59
> Failed 58/59 tests, 1.69% okay
> t\seqfeature....ok 2/48Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> <GEN0>
> line 72.
> t\seqfeature....dubious
> Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-48
> Failed 46/48 tests, 4.17% okay
> t\simpleseq.....ok 8/27Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> <GEN0>
> line 1.
> (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> at t\
> simpleseq.t line 45, <GEN0> line 1.
> (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> at t\
> simpleseq.t line 73, <GEN0> line 1.
> Undefined subroutine &Bio::Root::Root::debug called at
> E:\temp\bioperl-db\blib\l
> ib/Bio/DB/BioSQL/BaseDriver.pm line 410, <GEN0> line 1.
> t\simpleseq.....dubious
> Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 9-27
> Failed 19/27 tests, 29.63% okay
> t\species.......ok 2/65Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198.
> t\species.......dubious
> Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-65
> Failed 63/65 tests, 3.08% okay
> t\swiss.........ok 2/52Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> <GEN0>
> line 78.
> t\swiss.........dubious
> Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-52
> Failed 50/52 tests, 3.85% okay
> Failed Test Stat Wstat Total Fail Failed List of Failed
> ------------------------------------------------------------------
> ----------
> ---
> t\cluster.t 255 65280 160 158 98.75% 3-160
> t\comment.t 255 65280 11 9 81.82% 3-11
> t\dblink.t 255 65280 18 16 88.89% 3-18
> t\ensembl.t 255 65280 15 13 86.67% 3-15
> t\fuzzy2.t 255 65280 21 19 90.48% 3-21
> t\genbank.t 255 65280 18 16 88.89% 3-18
> t\locuslink.t 255 65280 110 107 97.27% 4-110
> t\ontology.t 255 65280 291 287 98.63% 5-291
> t\remove.t 255 65280 59 58 98.31% 2-59
> t\seqfeature.t 255 65280 48 46 95.83% 3-48
> t\simpleseq.t 255 65280 27 19 70.37% 9-27
> t\species.t 255 65280 65 63 96.92% 3-65
> t\swiss.t 255 65280 52 50 96.15% 3-52
> Failed 13/15 test scripts, 13.33% okay. 861/919 subtests failed,
> 6.31% okay.
> ******************************************************************
> **********
> ****
>
>
>
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Hilmar Lapp
> Sent: 09 October 2003 02:01
> To: Robert Roth
> Cc: BioPerl
> Subject: [Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl
>
>
> This is definitely related to the perl setup I'd claim. Have you been able
> to run the bioperl test suite without similar trouble?
>
> Again, I'm cc'ing the bioperl list in case anybody has seen this also and
> has clues as to what the cause is and how to remedy it.
>
> -hilmar
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
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