[Bioperl-l] make test!!

Nathan Haigh nathanhaigh at ukonline.co.uk
Sun Oct 24 04:00:26 EDT 2004 

Ops, must have been a problem with my web connection!

It actually gives the following output:

perl -w -I. t\Registry.t
1..12
ok 1
ok 2
ok 3
This Perl doesn't implement function getpwuid(). Skipping...

-------------------- WARNING ---------------------
MSG: No seqdatabase.ini file found in ~/.bioinformatics/
nor in /etc/bioinformatics/ nor in directory specified by
t/data/registry/flat;t/data/registry/bdb. Using web to get database registry from
http://www.open-bio.org/registry/seqdatabase.ini
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: Stored the default registry configuration in
/.bioinformatics/seqdatabase.ini
---------------------------------------------------
ok 4
not ok 5
# Failed test 5 in t\Registry.t at line 63

-------------------- WARNING ---------------------
MSG: No database with name testflat in Registry
---------------------------------------------------
not ok 6
# Failed test 6 in t\Registry.t at line 65
Can't call method "get_Seq_by_id" on an undefined value at t\Registry.t line 66, <FH> line 11.

I'm just going to debug this, and post further details!
Nathan

> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Nathan Haigh
> Sent: 23 October 2004 21:23
> To: 'Brian Osborne'; 'Bioperl'
> Subject: RE: [Bioperl-l] make test!!
> 
> I get the following error:
> 
> 
> perl -w -I. t\Registry.t
> 1..12
> ok 1
> ok 2
> ok 3
> This Perl doesn't implement function getpwuid(). Skipping...
> 
> -------------------- WARNING ---------------------
> MSG: No seqdatabase.ini file found in ~/.bioinformatics/
> nor in /etc/bioinformatics/ nor in directory specified by
> t/data/registry/flat;t/data/registry/bdb. Using web to get database registry from
> http://www.open-bio.org/registry/seqdatabase.ini
> ---------------------------------------------------
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: can't connect: IO::Socket::INET: Bad hostname 'www.open-bio.org'
> STACK: Error::throw
> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:328
> STACK: Bio::Root::HTTPget::getFH Bio/Root/HTTPget.pm:207
> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:128
> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:97
> STACK: t\Registry.t:57
> -----------------------------------------------------------
> 
> Nathan
> 
> > -----Original Message-----
> > From: Brian Osborne [mailto:brian_osborne at cognia.com]
> > Sent: 22 October 2004 22:12
> > To: nathanhaigh at ukonline.co.uk; 'Bioperl'
> > Subject: RE: [Bioperl-l] make test!!
> >
> > Nathan,
> >
> > Please replace your t/Registry.t with the attached Registry.t file and tell
> > me what happens after:
> >
> > >perl -w -I. t/Registry.t
> >
> > Brian O.
> >
> > -----Original Message-----
> > From: Nathan Haigh [mailto:nathanhaigh at ukonline.co.uk]
> > Sent: Thursday, October 21, 2004 7:59 AM
> > To: 'Brian Osborne'; 'Bioperl'
> > Subject: RE: [Bioperl-l] make test!!
> >
> > Ok, I've done some more testing (with the latest CVS 9am GMT) and here is
> > what I've found! I've run "namke test" with and without
> > BIOPERLDEBUG, and running individual tests using " perl -I. -w
> > t/test_name.t".
> >
> > Attached are 3 files with details of errors:
> > Errors.txt              - summary and details of failed tests, and other
> > tests with peculiar warnings etc
> > Errors_debug.txt        - same as errors.txt but with BIOPERLDEBUG set
> > Perl_test.txt           - individual tests run with BIOPERLDEBUG set, using
> > "perl -I. -w t/test_name.t"
> >
> > My System:
> > WinXP Pro
> > ActiveState Perl 5.8.0
> > Nmake 6.00.8168.0
> >
> > My Summary:
> > ESEfinder.t     - causes perl to crash on test 2 during "nmake test", but ok
> > in other tests!
> > Biblio_biofetch.t       - throws warning and exception when using
> > BIOPERLDEBUG, but doesn't appear in summary!
> > Index.t         - fails get_Seq_by_id ('AI129902') on lines 118 and 124
> > ProtPsm.t       - needs "plan tests" in test file changing to 5. When
> > running the individual test can't locate
> > Bio::Matrix::PSM::ProtMatrix
> > Registry.t      - several error including "No seqdatabase.ini file found", "
> > No database with name testflat in Registry"
> > Primaryqual.t   - Test returned status 255. and 'Can't locate object method
> > "header"' in individual test
> > seqread_fail.t  - gives an exception, is this supposed to happen?
> >
> > Hope this help to iron out bugs when running BioPerl on Windows!
> > Nathan
> >
> >
> > > -----Original Message-----
> > > From: Brian Osborne [mailto:brian_osborne at cognia.com]
> > > Sent: 20 October 2004 19:04
> > > To: nathanhaigh at ukonline.co.uk; 'Bioperl'
> > > Subject: RE: [Bioperl-l] make test!!
> > >
> > > Nathan,
> > >
> > > I noticed most of the Registry tests failing. I know what part of the
> > > problem is (getpwuid() not implemented in Windows/Activestate Perl) and I
> > > think I've fixed at least that part. Can you install the most recent
> > > Bio/DB/Registry.pm from bioperl-live and run t/Registry.t again?
> > >
> > > >perl -w -I. t/Registry.t
> > >
> > >
> > > 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 Nathan Haigh
> > > Sent: Wednesday, October 20, 2004 10:20 AM
> > > To: 'Bioperl'
> > > Subject: RE: [Bioperl-l] make test!!
> > >
> > > Apologise for all the pervious messages! I just wanted to get this onto
> > the
> > > mailing list:
> > >
> > > I have managed to do a "nmake test" (WinXP) on bioperl-live.
> > >
> > > System: WinXP Pro
> > > ActiveState Perl 5.8.0 build 804
> > > Nmake v6.00.8168.0
> > >
> > > A note beforehand:
> > > The error message I had previously got, and heard others have also
> > received
> > > on other OS's. That contain a "line too long" error when
> > > trying "make test", is due to the limitations of the particular OS.
> > Versions
> > > of ExtUtils::MakeMaker >= 6.06 (current version: 6.21)
> > > have got round this problem by splitting long command lines from Makefiles
> > > into a series of smaller commands.
> > >
> > > Test Summary:
> > > Failed Test      Stat Wstat Total Fail  Failed  List of Failed
> > > --------------------------------------------------------------------------
> > --
> > > ---
> > > t\Index.t          22  5632    41   21  51.22%  21-41
> > > t\Registry.t       22  5632    11    9  81.82%  3-11
> > > t\seqread_fail.t  255 65280    13    0   0.00%  ??
> > > 115 subtests skipped.
> > > Failed 3/192 test scripts, 98.44% okay. 30/8816 subtests failed, 99.66%
> > > okay.
> > > NMAKE : fatal error U1077: 'I:\Programming\Perl\Perl5.8.0\bin\perl.exe' :
> > > return code '0xff'
> > > Stop.
> > >
> > > Particulars:
> > > t\Index......................NOK 21Can't call method "length" on an
> > > undefined value at t\Index.t line 124, <GEN6> line
> > >  54.
> > > t\Index......................dubious
> > >         Test returned status 22 (wstat 5632, 0x1600)
> > > DIED. FAILED tests 21-41
> > >         Failed 21/41 tests, 48.78% okay
> > > t\Registry...................ok 2/11The getpwuid function is unimplemented
> > > at K:\Downloads\FlashGet\Software\Bioinform
> > > atics\BioPerl\1\bioperl-live\blib\lib/Bio/DB/Registry.pm line 116.
> > > t\Registry...................dubious
> > >         Test returned status 22 (wstat 5632, 0x1600)
> > > t\seqread_fail...............ok 1/13
> > > ------------- EXCEPTION: Bio::Root::Exception -------------
> > > MSG: BioFetch Error 4: ID [XXX111] not found in database
> > > [embl][http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[embl-id:
> > > XXX111]|[embl-acc:XXX111]+-ascii+-vn+2+-noSession].
> > > STACK: Error::throw
> > > STACK: Bio::Root::Root::throw
> > >
> > K:\Downloads\FlashGet\Software\Bioinformatics\BioPerl\1\bioperl-live\blib\li
> > > b/Bio/Root/R
> > > oot.pm:328
> > > STACK: Bio::DB::BioFetch::postprocess_data
> > >
> > K:\Downloads\FlashGet\Software\Bioinformatics\BioPerl\1\bioperl-live\blib\l
> > > ib/Bio/DB/BioFetch.pm:406
> > > STACK: Bio::DB::WebDBSeqI::get_seq_stream
> > >
> > K:\Downloads\FlashGet\Software\Bioinformatics\BioPerl\1\bioperl-live\blib\li
> > > b/Bio/DB/WebDBSeqI.pm:525
> > > STACK: Bio::DB::WebDBSeqI::get_Stream_by_id
> > > K:\Downloads\FlashGet\Software\Bioinformatics\BioPerl\1\bioperl-live\blib\
> > > lib/Bio/DB/WebDBSeqI.pm:287
> > > STACK: Bio::DB::WebDBSeqI::get_Seq_by_id
> > >
> > K:\Downloads\FlashGet\Software\Bioinformatics\BioPerl\1\bioperl-live\blib\li
> > > b
> > > /Bio/DB/WebDBSeqI.pm:153
> > > STACK: main::fetch t\seqread_fail.t:69
> > > STACK: t\seqread_fail.t:81
> > > -----------------------------------------------------------
> > > t\seqread_fail...............dubious
> > >         Test returned status 255 (wstat 65280, 0xff00)
> > >         after all the subtests completed successfully
> > >
> > >
> > > Nathan
> > >
> > > > -----Original Message-----
> > > > From: bioperl-l-bounces at portal.open-bio.org
> > > [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Aaron J.
> > Mackey
> > > > Sent: 14 October 2004 21:27
> > > > To: Bioperl
> > > > Subject: [Bioperl-l] make test!!
> > > > Importance: High
> > > >
> > > >
> > > > I've had only a very few people send me feedback about the current
> > > > state of bioperl-live "make test" on your favorite
> > > > old/crotchety/obscure platforms.  I'm writing the Change log and
> > > > thinking about branching, but I'm an experimentalist, I need data!
> > > >
> > > > Get a bioperl-live HEAD checkout, do a "cvs update -PAd" to make sure
> > > > you have everything, "make distclean" if you've built from the cvs
> > > > checkout before, and start from scratch with the usual litany: perl
> > > > Makefile.PL; make; [setenv BIOPERLDEBUG 1;] make test; email Aaron.
> > > >
> > > > Setting BIOPERLDEBUG is very noisy, but it's the end result I care
> > > > about, not so much all the verbiage (unless there's specific verbiage
> > > > related to the end result ...)
> > > >
> > > > Thanks,
> > > >
> > > > -Aaron
> > > >
> > > > _______________________________________________
> > > > Bioperl-l mailing list
> > > > Bioperl-l at portal.open-bio.org
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