[BioC] Problem with biomaRt::getSequence.

[Tanvir Ahamed [guest]]

Hi,
I can run the code some days ago . But cant run now. 

Problem 1: Output is ok
ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
utr5 = getSequence(chromosome=3, start=185514033, end=185535839, type="entrezgene",seqType="5utr", mart=ensembl) 
Output : 
                                                                                              5utr  entrezgene
                                                                             Sequence unavailable      10644
                                             GGAGCGCCGGGTACCGGGCCGGGGGAGCCGCGGGCTCTCGGGGAAGAGACGG      10644
3 GGGGGGCGGAGGAGGAGGAGAGACGAGGGCAGCGGAGGAGGCGAGGAGCGCCGGGTACCGGGCCGGGGGAGCCGCGGGCTCTCGGGGAAGAGACGG      10644
                                 CGGAGGAGGCGAGGAGCGCCGGGTACCGGGCCGGGGGAGCCGCGGGCTCTCGGGGAAGAGACGG      10644
                                                         No UTR is annotated for this transcript      10644
 
Problem 2:Problem is here
protein = getSequence(id=c(100, 5728),type="entrezgene",seqType="peptide", mart=ensembl)

Error in getBM(c(seqType, type), filters = type, values = id, mart = mart,  : 
  Query ERROR: caught BioMart::Exception::Database: Error during query execution: Can't create/write to file '/mnt/ephemeral0/mysqltmp/#sql_40a_0.MYI' (Errcode: 2)

I need help please.


 -- output of sessionInfo(): 

R version 3.0.0 (2013-04-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Bangla_Bangladesh.1252  LC_CTYPE=Bangla_Bangladesh.1252    LC_MONETARY=Bangla_Bangladesh.1252 LC_NUMERIC=C                      
[5] LC_TIME=Bangla_Bangladesh.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] seqinr_3.0-7   biomaRt_2.16.0

loaded via a namespace (and not attached):
[1] RCurl_1.95-4.1 tools_3.0.0    XML_3.96-1.1 

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