Dear Jari,
I will re-start using BSE. I tried for a little while a year ago and I used
BASE 1.2.17. Now That I will start again from scratch should I install BASE 2.4
or should I keep BASE 1.2.17. What is your advice?. Thankyou a lot.
Best regards,
Diana Bernal
Jari Häkkinen <[EMAIL PROTECTED]> escribió:
Hi Sergio,
We are looking in to this problem but have difficulty to reproduce the
error. We have tested the plier plugin with apt v1.6. Are you using the
latest apt release (1.8)? (Do 'apt-probeset-summarize --version' to get
the version information.)
Do you get a new (visible) node in the analysis tree in BASE after
running the plugin?
We would be happy if we could move this discussion to the ticket related
to this issue. Add comments to http://baseplugins.thep.lu.se/ticket/73
but remember to login as base/base to add comments.
Cheers,
Jari
Nicklas Nordborg wrote:
> Sergio Contrino wrote:
>> dear nicklas,
>> thank you for the prompt answer and apologies for the lack of info.
>> here the info requested.
>> thank you
>> sergio
>>
>> i am running a test base 2.3.2 on mysql 5.1.14-beta (i must apologies
>> again, i was thinking to be running on the reccomended 5.0)
>>
>> the stack (as in base report) is
>
> I think I partly know what is happening. There are two problems, the
> first causing the second.
>
> 1. The Plier plugin is creating a root bioassayset but is never
> inserting any data to it. If no data is inserted, then the missing table
> isn't created.
>
> 2. Before everything is committed to the database the root bioassayset
> tries to count the number spots that has been inserted. This fails
> because the table isn't there and there is no check if it exists at this
> place.
>
> Number 2 is a bug in the BASE core and should be easy to fix. This will
> be included in the 2.4 release in about two weeks.
>
> Why number 1 is happening is hard to tell. The Plier plug-in seems to
> execute without errors. Maybe there is something wrong with the output
> from the the 'apt-probeset-summarize' program. In that case, the plug-in
> will just ignore it and continue without inserting any data. I guess the
> developer of the Plier plug-in knows more about this...
>
> I'll add a ticket to the BASE plug-ins site about #1.
>
> /Nicklas
>
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--
Jari Hakkinen, PhD
Complex Systems Division mailto:[EMAIL PROTECTED]
Department of Theoretical Physics phone: +46 (0)46 2229347
Lund University fax: +46 (0)46 2229686
Solvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se
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