[Bioperl-l] Install help errors

snoze pa snoze.pa at gmail.com
Wed Jul 2 20:49:39 UTC 2008


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
>



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