[Bioperl-l] Install help errors

Hilmar Lapp hlapp at gmx.net
Sun Jul 6 23:10:24 UTC 2008


Thanks to everyone who chimed in on this report.

Snoze Pa - let us know if the responses didn't resolve the issue for  
you.

	-hilmar

On Jul 2, 2008, at 4:49 PM, snoze pa wrote:

> I used the latest rpm shipped with fedora 9.
>
> Next I removed the bioperl from fedora 9 and try to installed it from
> the CPAN.. it worked fine but thr bioperl-db again give me following
> messages using cpan. Seems nothing working properly!
>
> thanks a lot for your help.
>
>
>
> Test Summary Report
> -------------------
> t/01dbadaptor (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 19 tests but ran 0.
> t/02species   (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 65 tests but ran 0.
> t/03simpleseq (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 59 tests but ran 0.
> t/04swiss     (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 52 tests but ran 0.
> t/05seqfeature (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 48 tests but ran 0.
> t/06comment   (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 11 tests but ran 0.
> t/07dblink    (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 18 tests but ran 0.
> t/08genbank   (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 18 tests but ran 0.
> t/09fuzzy2    (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 21 tests but ran 0.
> t/10ensembl   (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 15 tests but ran 0.
> t/11locuslink (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 110 tests but ran 0.
> t/12ontology  (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 738 tests but ran 0.
> t/13remove    (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 59 tests but ran 0.
> t/14query     (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 18 tests but ran 0.
> t/15cluster   (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 160 tests but ran 0.
> t/16obda      (Wstat: 512 Tests: 0 Failed: 0)
>  Non-zero exit status: 2
>  Parse errors: Bad plan.  You planned 12 tests but ran 0.
> Files=16, Tests=0,  2 wallclock secs ( 0.09 usr  0.06 sys +  1.19 cusr
> 0.20 csys =  1.54 CPU)
> Result: FAIL
> Failed 16/16 test programs. 0/0 subtests failed.
>  SENDU/bioperl-db-1.5.2_100.tar.gz
>  ./Build test -- NOT OK
> //hint// to see the cpan-testers results for installing this module,  
> try:
>  reports SENDU/bioperl-db-1.5.2_100.tar.gz
> Warning (usually harmless): 'YAML' not installed, will not store
> persistent state
> Running Build install
>  make test had returned bad status, won't install without force
> Failed during this command:
> BIRNEY/bioperl-1.4.tar.gz                    : make_test NO
> SENDU/bioperl-db-1.5.2_100.tar.gz            : make_test NO
>
> On Wed, Jul 2, 2008 at 3:13 PM, Scott Cain <cain.cshl at gmail.com>  
> wrote:
>> 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
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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