[Bioperl-l] make test!!
Brian Osborne
brian_osborne at cognia.com
Fri Oct 22 17:11:55 EDT 2004
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
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
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