R: BioMart kicks me out every now and then
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@mauedealiceit-3511
Last seen 10.2 years ago
Well, it is not a systematic problem. If I restart my code from the element (miRNA) that was being processed when the interruption occurred .. then it works. I mean not only that miRNA is correctly processed but other new ones are. In thys case I can hardly trace back a bug in my code ... which I cannot exclude. Maura -----Messaggio originale----- Da: Wolfgang Huber [mailto:whuber@embl.de] Inviato: mar 27/10/2009 13.15 A: Sean Davis Cc: mauede@alice.it; Stefano Rovetta; Bioconductor List Oggetto: Re: [BioC] BioMart kicks me out every now and then Dear Maura how do you know it is BioMart and not your own code? Best wishes Wolfgang ------------------------------------------------------- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber ----------------------------------------- Sean Davis ha scritto: > On Tue, Oct 27, 2009 at 6:12 AM, <mauede@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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- -------------- tutti i telefonini TIM! [[alternative HTML version deleted]]
miRNA biomaRt miRNA biomaRt • 1.1k views
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@mauedealiceit-3511
Last seen 10.2 years ago
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. If a time limit does exist then I should try to implement some sort of cron process whose feasibility is questionable using a scripting language. I feel a solution can be found, on part of the code, maybe resorting to some C funtions linked to the R script. Right now I have a higher priority task but I will definitely get back to thir problem later on. Maura -----Messaggio originale----- Da: Sean Davis [mailto:seandavi@gmail.com] Inviato: mar 27/10/2009 11.45 A: mauede@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@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 tutti i telefonini TIM! [[alternative HTML version deleted]]
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On Tue, Oct 27, 2009 at 8:31 AM, <mauede@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@gmail.com <seandavi@gmail.com>] > Inviato: mar 27/10/2009 11.45 > A: mauede@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@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 > [[alternative HTML version deleted]]
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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 >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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