[Bioperl-l] Error retrieving sequence from BioSQL

Mon Oct 23 21:34:47 UTC 2006

Don't know what that particular error is, but it looks ActivePerl-related
(PPM generates HTML from the blib directory).  You may need to run 'nmake
clean' in between test cycles get rid of old blib and other files.

The carryover issue from old test runs was a definite problem.  Brian fixed
that in the bioperl-db CVS recently.  Also,  I tried Sendu's fixes from CVS
head to Bio::Root::Root and they seem to fix the problems with
Bio::Root::Root.  The issue came down to a use of indirect syntax (a bad
perl practice).  There are other errors popping up related to Bio::Species,
but these seem fixable at least.

I committed a few changes to bioperl-db CVS to fix 03simpleseq.t test
failures due to a lack of gzip on WinXP (I didn't see them b/c I had a copy
on GNU gzip in my path).  These should pass w/o problems now on WinXP.  

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

  _____  

From: Seth Johnson [mailto:johnson.biotech at gmail.com] 
Sent: Monday, October 23, 2006 4:22 PM
To: Chris Fields
Cc: bioperl-l
Subject: Re: Error retrieving sequence from BioSQL

Chris,

I have not cleaned my test database yet.  I'll purge it and redo the tests. 

This error keeps popping up in unexpected places while running nmake during
installation: 
 "Undefined subroutine &main::UpdateHTML_blib called at -e line 1. 
NMAKE : fatal error U1077: 'C:\WINDOWS\system32\cmd.exe' : return code
'0xff'"

Is there a way around it??

Seth

On 10/23/06, Chris Fields <cjfields at uiuc.edu> wrote:

Seth, 

Did you try this with a clean, taxonomy-installed database?  There may be
some junk left over tfrom the previous test runs.

I'm looking into it this week; it may not make the developer release but
we'll try to get it in.  BTW, the 02sinmpleseq.t test failures have to do
with a call to gzip.  I'll look into a workaround for that.  

Sendu has posted a Bio::Root::Root fix which does get rid of some bugs but
introduces others.  One alternative which I found works is cygwin, but
there's a catch: DBD-mysql is hard to install.  If it isn't one thing it's
another...

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

  _____  

From: Seth Johnson [mailto:johnson.biotech at gmail.com] 
Sent: Monday, October 23, 2006 11:37 AM
To: Chris Fields
Cc: bioperl-l
Subject: Re: Error retrieving sequence from BioSQL

Chris,

There's definite improvement:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Failed Test     Stat Wstat Total Fail  Failed  List of Failed
----------------------------------------------------------------------------
--- 
t/02species.t                 65    2   3.08%  63 65
t/03simpleseq.t    1   256    59  106 179.66%  7-59
t/04swiss.t                   52   14  26.92%  25 27-34 38-42
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

There's some weirdness going on during the 'swiss.t' test.  It almost seems
to me that expectations of some tests are swapped (27 & 39, 28 & 40, 29 &
41, 31 & 27, 32 & 28, 33 & 29, 39 & 31): 
================================
not ok 25
# Test 25 got: '10097078' (t/04swiss.t at line 79)
#    Expected: '91309150'
ok 26
not ok 27
# Test 27 got: 'Jiang,J., Zhang,Y., Krainer,A.R. and Xu,R.M.' (t/04swiss.t
at line 85) 
#    Expected: 'Krainer,A.R., Mayeda,A., Kozak,D. and Binns,G.'
not ok 28
# Test 28 got: 'Crystal structure of human p32, a doughnut-shaped acidic
mitochondrial matrix protein' (t/04swiss.t at line 86)
#    Expected: 'Functional expression of cloned human splicing factor SF2:
homology to RNA-binding proteins, U1 70K, and Drosophila splicing
regulators' 
not ok 29
# Test 29 got: 'Proc. Natl. Acad. Sci. U.S.A. 96 (7), 3572-3577 (1999)'
(t/04swiss.t at line 87)
#    Expected: 'Cell 66 (2), 383-394 (1991)'
not ok 30
# Test 30 got: <UNDEF> (t/04swiss.t at line 88) 
#    Expected: '91309150'
not ok 31
# Test 31 got: 'Krainer,A.R., Mayeda,A., Kozak,D. and Binns,G.' (t/04swiss.t
at line 85 fail #2)
#    Expected: 'Honore,B., Madsen,P., Rasmussen,H.H., Vandekerckhove,J.,
Celis, J.E. and Leffers,H.'
not ok 32
# Test 32 got: 'Functional expression of cloned human splicing factor SF2:
homology to RNA-binding proteins, U1 70K, and Drosophila splicing
regulators' (t/04swiss.t at line 86 fail #2) 
#    Expected: 'Cloning and expression of a cDNA covering the complete
coding region of the P32 subunit of human pre-mRNA splicing factor SF2'
not ok 33
# Test 33 got: 'Cell 66 (2), 383-394 (1991)' (t/04swiss.t at line 87 fail
#2) 
#    Expected: 'Gene 134 (2), 283-287 (1993)'
not ok 34
# Test 34 got: <UNDEF> (t/04swiss.t at line 88 fail #2)
#    Expected: '94085792'
ok 35
ok 36
ok 37
not ok 38
# Test 38 got: <UNDEF> (t/04swiss.t at line 88 fail #3) 
#    Expected: '94253723'
not ok 39
# Test 39 got: 'Honore,B., Madsen,P., Rasmussen,H.H., Vandekerckhove,J.,
Celis,J.E. and Leffers,H.' (t/04swiss.t at line 85 fail #4)
#    Expected: 'Jiang,J., Zhang,Y., Krainer, A.R. and Xu,R.M.'
not ok 40
# Test 40 got: 'Cloning and expression of a cDNA covering the complete
coding region of the P32 subunit of human pre-mRNA splicing factor SF2'
(t/04swiss.t at line 86 fail #4)
#    Expected: 'Crystal structure of human p32, a doughnut-shaped acidic
mitochondrial matrix protein' 
not ok 41
# Test 41 got: 'Gene 134 (2), 283-287 (1993)' (t/04swiss.t at line 87 fail
#4)
#    Expected: 'Proc. Natl. Acad. Sci. U.S.A. 96 (7), 3572-3577 (1999)'
not ok 42
# Test 42 got: <UNDEF> (t/04swiss.t at line 88 fail #4) 
#    Expected: '99199225'
==============================

On 10/20/06, Chris Fields < cjfields at uiuc.edu <mailto:cjfields at uiuc.edu> >
wrote:

Seth,

Did you work out the problem here?  There was a recent CVS update to OBDA
tests (16obda.t) that fixed similar problems on Mac OS X.  Old OBDA tests
apparently left data from tests in the database, which caused problems with 
repeated test runs.

Chris

> > -----Original Message-----
> > From: bioperl-l-bounces <at> lists.open-bio.org [mailto: bioperl-l-
<mailto:bioperl-l-> 
> > bounces <at> lists.open-bio.org] On Behalf Of Seth Johnson
> > Sent: Saturday, September 30, 2006 6:35 PM 
> > To: Hilmar Lapp
> > Cc: Chris Fields; Bioperl List
> > Subject: Re: [Bioperl-l] Error retrieving sequence from BioSQL
> >
> > Here're complete test details:
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> ...
>
> > FAILED tests 10-12
> >     Failed 3/12 tests, 75.00% okay
> > Failed Test     Stat Wstat Total Fail  Failed  List of Failed
> >
> --------------------------------------------------------------------------

> > -----
> > t\02species.t                 65    2   3.08%  63 65
> > t\03simpleseq.t    1   256    59  106 179.66%  7-59
> > t\04swiss.t                   52   14  26.92%  25 27-34 38-42 
> > t\12ontology.t     2   512   738 1471 199.32%  3-738
> > t\16obda.t                    12    3  25.00%  10-12
> > _______________________________________________
> > Bioperl-l mailing list 
> > Bioperl-l <at> lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
<http://lists.open-bio.org/mailman/listinfo/bioperl-l> 
>
>

-- 
Best Regards,

Seth Johnson
Senior Bioinformatics Associate

Ph: (202) 470-0900
Fx: (775) 251-0358 