[BioC] R: BioMart kicks me out every now and then

[Steffen at stat.Berkeley.EDU]

Hi Maura,

Are you trying to use biomaRt queries in a loop?  This is strongly
discouraged and will indeed result in your script stopping randomly.
biomaRt is made to do batch queries. So if you are using it in a loop, try
to rewrite your queries into one batch biomaRt query and then loop over
the result in R.  If you need help with this, give us the exact query you
are trying to perform.

Cheers,
Steffen

> On Tue, Oct 27, 2009 at 8:31 AM, <mauede at alice.it> wrote:
>
>>  I do not have any other information to add. To my experience these
>> interruptions occur randomly. I daresay, perhaps, the connection has a
>> time
>> limit
>> or is sensitive to the queries load.
>>
> Reproducible code example, or at least code and error message?
> sessionInfo()?  Any message to the list asking for help with an error
> NEEDS
> to have these two elements.
>
> Sean
>
> -----Messaggio originale-----
>> Da: Sean Davis [mailto:seandavi at gmail.com <seandavi at gmail.com>]
>> Inviato: mar 27/10/2009 11.45
>> A: mauede at alice.it
>> Cc: Bioconductor List; Stefano Rovetta
>> Oggetto: Re: [BioC] BioMart kicks me out every now and then
>>
>> On Tue, Oct 27, 2009 at 6:12 AM, <mauede at alice.it> wrote:
>>
>> > **** CURRENT miRNA BEING PROCESSED:  hsa-miR-548d-5p   ****
>> >
>> >
>> >  OPEN NEW CONNECTION ON FILE:
>> hsa-miR-548d-5p_V_MirBase_FastaFiles.txt
>> >
>> >  **** WRITE 3UTR SEQUENCE TO FILE:
>> > hsa-miR-548d-5p_V_MirBase_FastaFiles.txt  ****
>> > Error in value[[3L]](cond) :
>> >  Request to BioMart web service failed. Verify if you are still
>> connected
>> > to the internet.  Alternatively the BioMart web service is temporarily
>> down.
>> > In addition: Warning message:
>> > In if (processed > 0) { :
>> >  the condition has length > 1 and only the first element will be used
>> > >
>> > Maura
>> >
>> >
>> Hi, Maura.  Is this email meant as a question or an observation?  If it
>> is
>> meant as a question, there is no useful information in this post to
>> allow
>> people to help.  You should try to follow the directions in the posting
>> guide before posting to the list.
>>
>> Sean
>>
>>
>>
>> Alice Messenger ;-) chatti anche con gli amici di Windows Live Messenger
>> e
>> tutti i telefonini TIM!
>> Vai su
>> http://maileservizi.alice.it/alice_messenger/index.html?pmk=footer
>>
>
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