[Bioperl-l] Install help errors
snoze pa
snoze.pa at gmail.com
Mon Jul 7 16:23:21 UTC 2008
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 :
> ===========================================================
>
>
>
>
More information about the Bioperl-l
mailing list