[BioC] connecting to ensembl

[Straubhaar, Juerg]

Hi Herve,

code:

library(biomaRt)
mart    <- useMart("ensembl","rnorvegicus_gene_ensembl")
attr.g  <- c("rgd_symbol","ensembl_gene_id","chromosome_name","start_position",
          "end_position","strand")
ensGene <- getBM(attributes=attr.g,mart=mart)

I run the code on the commandline

R --no-save < processSeq.R 1>process.out 2>error.out

process.out contains 

LOC682397	ENSRNOG00000043314	13	1120899	1121213	-1
LOC304725	ENSRNOG00000031539	13	1192186	2293551	-1
	ENSRNOG00000031539	13	1192186	2293551	-1
	ENSRNOG00000028603	13	3174383	3175216	1
	ENSRNOG00000030028	13	4377731	4379174	-1
	ENSRNOG00000040235	13	4866302	4866586	-1
	ENSRNOG00000040233	13	5486651	5487388	1
RGD1561440	ENSRNOG00000033336	13	5488973	5493293	-1
	ENSRNOG00000021163	13	5972234	6066767	-1
	ENSRNOG00000030239	13	7099478	7102595	1
...

all 36669 rows from getBM function which should be stored in the ensGene variable. The ensGene variable is empty
because of the error.

error.out contains

Error in getBM(attributes = attr.g, mart = mart) : 
  The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list.

Connection worked fine until beginning of this week when error appeared.

> sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] C

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

other attached packages:
 [1] annaffy_1.22.0       KEGG.db_2.4.5        GO.db_2.4.5         
 [4] AnnotationDbi_1.12.1 ShortRead_1.8.2      Rsamtools_1.2.3     
 [7] Biostrings_2.18.4    GenomicRanges_1.2.3  Genominator_1.4.2   
[10] GenomeGraphs_1.10.0  biomaRt_2.6.0        IRanges_1.8.9       
[13] RSQLite_0.9-4        DBI_0.2-5            DESeq_1.2.1         
[16] locfit_1.5-6         lattice_0.19-26      akima_0.5-4         
[19] Biobase_2.10.0       multicore_0.1-5     

loaded via a namespace (and not attached):
 [1] RColorBrewer_1.0-2 RCurl_1.6-1        XML_3.4-0          annotate_1.28.1   
 [5] genefilter_1.32.0  geneplotter_1.28.0 hwriter_1.3        splines_2.12.2    
 [9] survival_2.36-5    xtable_1.5-6 


Kind regards,
Juerg Straubhaar
UMASS Med School
________________________________________
From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] On Behalf Of Hervé Pagès [hpages at fhcrc.org]
Sent: Tuesday, May 17, 2011 9:50 PM
To: s.kroeger at drfz.de
Cc: bioconductor at r-project.org
Subject: Re: [BioC] connecting to ensembl

Hi Stefan,

On 11-05-17 01:57 AM, Stefan Kroeger wrote:
> Does anybody else has problem with connecting to ensembl (since yesterday)?
>
> example code:
> myMart<- useMart("ensembl", dataset = "mmusculus_gene_ensembl")

Please show the output or the error message you get.

Yes we see problems in our daily build reports e.g.


http://bioconductor.org/checkResults/2.8/bioc-LATEST/GenomicFeatures/lamb1-checksrc.html

AFAICT for at least the last couple of days, biomaRt and all the
packages that depend on it seem to have problems to connect to the
ensembl Mart during the builds :-/

H.

>
> Best
>   Stefan
>
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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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