[MOBY-dev] help: local registry installation
Mark Wilkinson
markw at illuminae.com
Fri Jun 1 16:23:01 UTC 2007
Ah! Yes, that's likely the cause.
We had problems last week at TIGR also using an older version of
SOAP::Lite. I should update the Makefile to ensure that it is properly
listing .69 as a requirement... luckily, SOAP::Lite no longer attempts to
upgrade your Perl installation when it installs itself :-)
M
On Thu, 31 May 2007 12:01:29 -0700, Pieter Neerincx
<Pieter.Neerincx at wur.nl> wrote:
> Hi,
>
> I also didn't see this specific case before, but it looks like a
> double encoded CDATA section. We've had problems with double encoded
> stuff before due to the way some versions of SOAP::Lite were handling
> encoding/decoding. If you are running SOAP::Lite < 0.69 please
> upgrade to 0.69. If you are running something more recent please let
> us know. Might be a new S::L peculiarity in that case...
>
> Cheers,
>
> Pi
>
>
> On 31 May 2007, at 18:06, Mark Wilkinson wrote:
>
>> Never seen that error before...
>>
>> perhaps check that your LibXML C libraries are up-to-date? They
>> are used
>> by the XML::LibXML module that Moby uses for XML parsing.
>>
>> M
>>
>>
>>
>> On Wed, 30 May 2007 20:12:32 -0700, Barboza, Lord Hendrix (IRRI)
>> <L.Barboza at cgiar.org> wrote:
>>
>>> I have already got and installed the biomoby code in the server. Then
>>> running the "make test" give me this result:
>>>
>>>
>>> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
>>> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
>>>
>>> t/Central.....................ok
>>>
>>>
>>> t/Client-Central..............ok 22/0:7: parser error : Sequence
>>> ']]>'
>>> not allowed in content
>>>
>>> ]]>]]></message>
>>>
>>> ^
>>>
>>> :7: parser error : internal error
>>>
>>> ]]>]]></message>
>>>
>>> ^
>>>
>>> :7: parser error : Extra content at the end of the document
>>>
>>> ]]>]]></message>
>>>
>>> ^
>>>
>>> at /usr/local/moby-live/Perl/blib/lib/MOBY/Client/Central.pm line
>>> 2107
>>>
>>> t/Client-Central..............ok 23/0# Looks like your test died just
>>> after 23.
>>>
>>> t/Client-Central..............dubious
>>>
>>>
>>> Test returned status 255 (wstat 65280, 0xff00)
>>>
>>> after all the subtests completed successfully
>>>
>>> t/Client-CollectionArticle....ok
>>>
>>>
>>> t/Client-OntologyServer.......ok
>>>
>>>
>>> t/Client-Registration.........ok
>>>
>>>
>>> t/Client-SecondaryArticle.....ok
>>>
>>>
>>> t/Client-Service..............ok 2/0:7: parser error : Sequence ']]>'
>>> not allowed in content
>>>
>>> ]]>]]></message>
>>>
>>> ^
>>>
>>> :7: parser error : internal error
>>>
>>> ]]>]]></message>
>>>
>>> ^
>>>
>>> :7: parser error : Extra content at the end of the document
>>>
>>> ]]>]]></message>
>>>
>>> ^
>>>
>>> at /usr/local/moby-live/Perl/blib/lib/MOBY/Client/Central.pm line
>>> 2107
>>>
>>> # Looks like your test died just after 2.
>>>
>>> t/Client-Service..............dubious
>>>
>>>
>>> Test returned status 255 (wstat 65280, 0xff00)
>>>
>>> after all the subtests completed successfully
>>>
>>> t/Client-ServiceInstance......ok
>>>
>>>
>>> t/Client-SimpleArticle........ok
>>>
>>>
>>> t/CommonSubs..................ok
>>>
>>>
>>> t/Config......................skipped
>>>
>>> all skipped: Required only when you have your own local MOBY
>>> Central
>>>
>>> t/CrossReference..............ok
>>>
>>>
>>> t/Template....................ok
>>>
>>>
>>> Failed Test Stat Wstat Total Fail Failed List of Failed
>>>
>>> ---------------------------------------------------------------------
>>> ---
>>> -------
>>>
>>> t/Client-Central.t 255 65280 23 0 0.00% ??
>>>
>>> t/Client-Service.t 255 65280 2 0 0.00% ??
>>>
>>> 1 test skipped.
>>>
>>> Failed 2/13 test scripts, 84.62% okay. 0/235 subtests failed, 100.00%
>>> okay.
>>>
>>> make: *** [test_dynamic] Error 255
>>>
>>> lbarboza at cropwiki:/usr/local/moby-live/Perl$ <MOBYRegistration>
>>>
>>> -bash: syntax error near unexpected token `newline'
>>>
>>>
>>>
>>> I am using perl v5.8.4. pls help
>>>
>>>
>>> thanks
>>>
>>>
>>> Lord Hendrix A. Barbozax`
>>>
>>> Programmer - Web Services
>>>
>>> Crop Research Informatics Laboratory (CRIL)
>>>
>>>
>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>>
>>
>> --
>> --
>> Mark Wilkinson
>> Assistant Professor, Dept. Medical Genetics
>> University of British Columbia
>> PI Bioinformatics
>> iCAPTURE Centre, St. Paul's Hospital
>> Tel: 604 682 2344 x62129
>> Fax: 604 806 9274
>>
>> ***CONFIDENTIALITY NOTICE***
>> This electronic message is intended only for the use of the
>> addressee and
>> may contain information that is privileged and confidential. Any
>> dissemination, distribution or copying of this communication by
>> unauthorized individuals is strictly prohibited. If you have
>> received this
>> communication in error, please notify the sender immediately by reply
>> e-mail and delete the original and all copies from your system.
>>
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> -------------------------------------------------------------
> Wageningen University and Research centre (WUR)
> Laboratory of Bioinformatics
> Transitorium (building 312) room 1034
>
> Dreijenlaan 3
> 6703 HA Wageningen
> The Netherlands
>
> phone: 0317-483 060
> fax: 0317-483 584
> mobile: 06-143 66 783
> mail: pieter.neerincx at wur.nl
> skype: pieter.online
> -------------------------------------------------------------
>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
--
--
Mark Wilkinson
Assistant Professor, Dept. Medical Genetics
University of British Columbia
PI Bioinformatics
iCAPTURE Centre, St. Paul's Hospital
Tel: 604 682 2344 x62129
Fax: 604 806 9274
***CONFIDENTIALITY NOTICE***
This electronic message is intended only for the use of the addressee and
may contain information that is privileged and confidential. Any
dissemination, distribution or copying of this communication by
unauthorized individuals is strictly prohibited. If you have received this
communication in error, please notify the sender immediately by reply
e-mail and delete the original and all copies from your system.
More information about the MOBY-dev
mailing list