[Bioperl-l] make test!!

Wed Oct 20 14:04:25 EDT 2004

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
>
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