[Bioperl-l] make test!!

Nathan Haigh nathanhaigh at ukonline.co.uk
Wed Oct 20 10:15:27 EDT 2004



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'




t\Index......................NOK 21Can't call method "length" on an undefined value at t\Index.t line 124, <GEN6> line



        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.


        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:


STACK: Error::throw

STACK: Bio::Root::Root::throw K:\Downloads\FlashGet\Software\Bioinformatics\BioPerl\1\bioperl-live\blib\lib/Bio/Root/R


STACK: Bio::DB::BioFetch::postprocess_data K:\Downloads\FlashGet\Software\Bioinformatics\BioPerl\1\bioperl-live\blib\l


STACK: Bio::DB::WebDBSeqI::get_seq_stream K:\Downloads\FlashGet\Software\Bioinformatics\BioPerl\1\bioperl-live\blib\li


STACK: Bio::DB::WebDBSeqI::get_Stream_by_id K:\Downloads\FlashGet\Software\Bioinformatics\BioPerl\1\bioperl-live\blib\


STACK: Bio::DB::WebDBSeqI::get_Seq_by_id K:\Downloads\FlashGet\Software\Bioinformatics\BioPerl\1\bioperl-live\blib\lib


STACK: main::fetch t\seqread_fail.t:69

STACK: t\seqread_fail.t:81



        Test returned status 255 (wstat 65280, 0xff00)

        after all the subtests completed successfully





> -----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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