[Bioperl-l] make test!!

Nathan Haigh nathanhaigh at ukonline.co.uk
Thu Oct 21 05:29:27 EDT 2004


I appear to have Fcntl.pm included (version 1.04).

I'll run the latest index tests though!

Nathan

> -----Original Message-----
> From: Brian Osborne [mailto:brian_osborne at cognia.com]
> Sent: 20 October 2004 21:56
> To: nathanhaigh at ukonline.co.uk; 'Bioperl'
> Subject: RE: [Bioperl-l] make test!!
> 
> Nathan,
> 
> My guess is that your ActiveState distribution doesn't include Fcntl.pm,
> which is used by Bio::DB::FileCache. I've changed Index.t to account for
> this possibility - can you test the latest t/Index.t?
> 
> >perl -I. -w t/Index.t
> 
> Thanks again,
> 
> 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
> >
> > _______________________________________________
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> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
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