[BioC] BioMart error

[Steffen at stat.Berkeley.EDU]

Hi,

Would it be possible to include the query you were attempting that
generated this error?

Steffen

>
>  OPEN NEW CONNECTION ON FILE:   hsa-miR-31_V_MirBase_FastaFiles.txt
>
>  **** WRITE 3UTR SEQUENCE TO FILE:   hsa-miR-31_V_MirBase_FastaFiles.txt
> ****
>
> Error in getBM(attributes = c("hgnc_symbol", "ensembl_gene_id",
> "refseq_dna",  :
>   Query ERROR: caught BioMart::Exception::Database: Could not connect to
> mysql database ensembl_mart_56: DBI
> connect('database=ensembl_mart_56;host=martdb.ensembl.org;port=5316','anonymous',...)
> failed: Can't connect to MySQL server on 'martdb.ensembl.org' (110) at
> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm
> line 98
>
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>  [1] microRNA_1.2.0    Rlibstree_0.3-2   gdata_2.4.2       CORNA_1.2
>  [5] XML_2.5-1         GEOquery_2.8.0    RCurl_0.98-1      bitops_1.0-4.1
>  [9] Biostrings_2.12.7 IRanges_1.2.3     biomaRt_2.0.0     Biobase_2.4.1
> [13] JGR_1.6-7         iplots_1.1-3      JavaGD_0.5-2      rJava_0.6-3
>
> loaded via a namespace (and not attached):
> [1] gtools_2.6.1
>
>
>
>
> tutti i telefonini TIM!
>
>
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