[Bioperl-l] Install help errors

Hilmar Lapp hlapp at gmx.net
Mon Jul 7 20:12:32 UTC 2008


You may use any name for the database - is there some piece of  
documentation that prompted you to conclude that this parameter isn't  
under your control? There should be a command-line parameter (-- 
namespace) in load_seqdatabase.pl

	-hilmar

On Jul 7, 2008, at 12:23 PM, snoze pa wrote:

> Dear Users,
> Thank you very much for you timely support. I highly appreciate your
> help in installing the software.  Meanwhile during the  installation
> of  bioperl-db and  loading load_seqdatabase.pl, it ask me to use the
> dbname "biosql" while the database created in during  bioperl
> installation is "bioseqdb". Shall I use bioseqdb instead of biosql as
> dbname.
> Thank you,
> s
>
>
> On Sun, Jul 6, 2008 at 6:10 PM, Hilmar Lapp <hlapp at gmx.net> wrote:
>> 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
>>
>> --
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>>
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-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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