[Bioperl-l] About to tag the last RC...

Wed Jan 14 14:46:47 UTC 2009

Hi,

I tested trunk r15372 (with network/DB tests) on:

- Perl v5.10.0 built for i486-linux-gnu-thread-multi
- Ubuntu 8.10
- Linux 2.6.27-11-generic #1 SMP

Apart from some warnings, I had some problems with Bio::DB::MeSH

Test Summary Report
-------------------
t/RemoteDB/DB                            (Wstat: 768 Tests: 116 Failed: 3)
  Failed tests:  114-116
  Non-zero exit status: 3
Files=323, Tests=19009, 544 wallclock secs ( 5.23 usr  1.21 sys + 209.70
cusr 11.88 csys = 228.02 CPU)
Result: FAIL
Failed 1/323 test programs. 3/19009 subtests failed.

Specifically:

t/RemoteDB/DB................................104/116 Use of uninitialized
value $desc in substitution (s///) at
/usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 267.
Use of uninitialized value $desc in substitution (s///) at
/usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 268.
Use of uninitialized value $name in regexp compilation at
/usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282.
Use of uninitialized value $name in regexp compilation at
/usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282.
Use of uninitialized value $name in regexp compilation at
/usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282.
t/RemoteDB/DB................................114/116
#   Failed test at t/RemoteDB/DB.t line 386.
#          got: '0'
#     expected: '2'
Use of uninitialized value $desc in substitution (s///) at
/usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 267.
Use of uninitialized value $desc in substitution (s///) at
/usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 268.
Use of uninitialized value $name in regexp compilation at
/usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282.
Use of uninitialized value $name in regexp compilation at
/usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282.
Use of uninitialized value $name in regexp compilation at
/usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282.
Use of uninitialized value $name in regexp compilation at
/usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282.
Use of uninitialized value $name in regexp compilation at
/usr/local/home/davis/Desktop/bioperl-live-trunk/Bio/DB/MeSH.pm line 282.
t/RemoteDB/DB................................115/116
#   Failed test at t/RemoteDB/DB.t line 389.
#          got: undef
#     expected: 'Thrombus formation in an intracranial venous sinus,
including the superior sagittal, cavernous, lateral, and petrous sinuses.
Etiologies include thrombosis due to infection,  DEHYDRATION, coagulation
disorders (see  THROMBOPHILIA), and  CRANIOCEREBRAL TRAUMA.'

#   Failed test at t/RemoteDB/DB.t line 390.
#          got: undef
#     expected: 'D012851'
# Looks like you failed 3 tests of 116.
t/RemoteDB/DB................................ Dubious, test returned 3
(wstat 768, 0x300)
 Failed 3/116 subtests
    (less 17 skipped subtests: 96 okay)

Cheers,
Chad

On Wed, Jan 14, 2009 at 14:28, Chris Fields <cjfields at illinois.edu> wrote:

> Yeah, the svggraph.t warning is something out of our control.  I googled
> the error and found it's a general problem with SVG::Graph, so I'll let
> Allen know.  I'll see if I can work out the other warning.
>
> The HIV.t warnings are sporadic and seem less frequent since last night.  I
> noticed the HIV database migrated RDBMS yesterday so it may be related to
> that (Mark Jensen, the HIV modules author, is aware of the problem).
>
> Thanks Dave!
>
> -c
>
>
> On Jan 14, 2009, at 3:53 AM, Dave Messina wrote:
>
>  Test report on trunk r15372, perl 5.8.8, CentOS 5.2, install all optional
>> modules, install all scripts, do network tests.
>>
>> All passed -- just saw two minor warnings, one from Bio::DB::Registry and
>> the same svggraph one as before.
>>
>> Dave
>>
>>
>>
>>
>> t/LocalDB/Registry.............................1/14
>> --------------------- WARNING ---------------------
>> MSG: Couldn't call new_from_registry() on [Bio::DB::Flat]
>>
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: you must specify an indexing scheme
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
>> STACK: Bio::DB::Flat::new Bio/DB/Flat.pm:160
>> STACK: Bio::DB::Flat::new_from_registry Bio/DB/Flat.pm:252
>> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:164
>> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:95
>> STACK: t/LocalDB/Registry.t:51
>> -----------------------------------------------------------
>>
>> ---------------------------------------------------
>> t/LocalDB/Registry.............................ok
>>
>>
>>
>> t/Tree/TreeIO/svggraph.........................1/4 Use of uninitialized
>> value in join or string at /afs/pdc.kth.se/home/d/dmessina/lib/perl5/site_perl/5.8.8/SVG/Element.pm
>> line 1195, <GEN0> line 1.
>> t/Tree/TreeIO/svggraph.........................ok
>>
>>
>>
>> All tests successful.
>> Files=322, Tests=20356, 545 wallclock secs ( 5.25 usr  0.87 sys + 173.39
>> cusr 26.97 csys = 206.48 CPU)
>> Result: PASS
>>
>>
>>
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