[Bioperl-l] Install help errors

[Scott Cain]

Hello,

When you say you installed the BioPerl RPM, do you mean the one at
biopackages.net?  It is very old and the likely problem you are
running into is that it is too old to work with the version of BioSQL
you have.

Scott


On Wed, Jul 2, 2008 at 3:56 PM, snoze pa <snoze.pa at gmail.com> wrote:
> Dear Users,
>  I am trying to install bioperl in fedora machine. I am using
> precompiled rpm from fedora repo. it is installed. Next I download the
> biosql and put in a dir /usr/local/biosql
> create a database bioseqdb and load the scema.
>
> However the bioperl-db is not working.. it is giving lots of error. I
> used CPAN and also the perl Build.PL. following are the results
>
> Please help me.
> thank you.
>
>
> Test Summary Report
> -------------------
> t/04swiss     (Wstat: 65280 Tests: 5 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 52 tests but ran 5.
> t/05seqfeature (Wstat: 65280 Tests: 3 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 48 tests but ran 3.
> t/06comment   (Wstat: 65280 Tests: 2 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 11 tests but ran 2.
> t/07dblink    (Wstat: 65280 Tests: 2 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 18 tests but ran 2.
> t/08genbank   (Wstat: 65280 Tests: 2 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 18 tests but ran 2.
> t/09fuzzy2    (Wstat: 65280 Tests: 2 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 21 tests but ran 2.
> t/10ensembl   (Wstat: 65280 Tests: 2 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 15 tests but ran 2.
> t/11locuslink (Wstat: 65280 Tests: 4 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 110 tests but ran 4.
> t/12ontology  (Wstat: 65280 Tests: 4 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 738 tests but ran 4.
> t/13remove    (Wstat: 0 Tests: 4 Failed: 1)
>  Failed test:  4
>  Parse errors: Bad plan.  You planned 59 tests but ran 4.
> t/15cluster   (Wstat: 65280 Tests: 5 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 160 tests but ran 5.
> t/16obda      (Wstat: 65280 Tests: 2 Failed: 0)
>  Non-zero exit status: 255
>  Parse errors: Bad plan.  You planned 12 tests but ran 2.
> Files=16, Tests=198, 26 wallclock secs ( 0.21 usr  0.07 sys + 22.81
> cusr  1.25 csys = 24.34 CPU)
> Result: FAIL
> Failed 12/16 test programs. 1/198 subtests failed.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D. cain.cshl at gmail.com
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory