[Bioperl-l] Error retrieving sequence from BioSQL

Seth Johnson johnson.biotech at gmail.com
Mon Oct 23 17:22:13 EDT 2006


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> 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-
> > > 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
> >
> >
>



-- 
Best Regards,


Seth Johnson
Senior Bioinformatics Associate

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


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