[Bioperl-l] Package status for 1.5.2

Sendu Bala bix at sendu.me.uk
Mon Sep 25 08:47:44 EDT 2006


Sendu Bala wrote:
> Brian Osborne wrote:
>> Let's take these one at a time, starting with t/Graph-MD5 (I'm not seeing
>> any of these errors so you'll have to test, sorry about that). I've changed
>> 'eval { require Graph; };' to 'eval { require Graph::Undirected; };'. Does
>> this help?
> 
> I compared my copy of Graph.pm (my command-line CPAN claims that 0.78 is 
> the latest version) to the one I could find via search.cpan.org (v0.80) 
> and they're nothing alike. Mine is just

Well, clearly 0.78 has issues so you might want to mention that in the 
documentation. Apparently the UK CPAN mirrors at least are out of date; 
I've removed mirrors from my CPAN urllist to get things direct from 
perl.org and now have 0.80 installed:

make test
PERL_DL_NONLAZY=1 /usr/bin/perl5.8.8 "-MExtUtils::Command::MM" "-e" 
"test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/Edge...........ok 

t/Graph-MD5......ok 

t/Graph-Seq......ok 

t/Interaction....ok 

t/IO_dip_tab.....ok 

t/IO_psi.........ok 1/21# Test 7 got: "pylori 26695" (t/IO_psi.t at line 
60)
#   Expected: "Helicobacter pylori 26695"
#  t/IO_psi.t line 60 is: ok 
$proteins[0]->species->binomial,"Helicobacter pylori 26695";
t/IO_psi.........NOK 7# Test 16 got: "virus 40" (t/IO_psi.t at line 81) 

#    Expected: "Simian virus 40"
#  t/IO_psi.t line 81 is: ok $proteins[0]->species->binomial,"Simian 
virus 40";
t/IO_psi.........FAILED tests 7, 16 

         Failed 2/21 tests, 90.48% okay
t/Node...........ok 

t/ProteinNet.....ok 

Failed Test Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/IO_psi.t                21    2   9.52%  7 16
Failed 1/8 test scripts, 87.50% okay. 2/296 subtests failed, 99.32% okay.
make: *** [test_dynamic] Error 255

So this is 'just' another taxonomy issue. I'll look into it. Do 
you/anyone want to see network tagged and distributed alongside core 1.5.2?


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