[Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl
Brian Osborne
brian_osborne at cognia.com
Thu Oct 9 08:44:26 EDT 2003
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#windows/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
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