biomaRt not working?
1
1
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s.corley ▴ 30
@scorley-6735
Last seen 4.8 years ago
Australia

 

I am having trouble using biomaRt.  Any ideas as to what might be happening?

Error message below.

Thanks

> library(biomaRt)

> listMarts(host="www.ensembl.org")
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Entity 'nbsp' not defined
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Entity 'nbsp' not defined
> human<-useMart(host="www.ensembl.org", "ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl")
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Entity 'nbsp' not defined
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Entity 'nbsp' not defined
> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.4 (El Capitan)

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

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

other attached packages:
[1] biomaRt_2.28.0 edgeR_3.14.0   limma_3.28.5  

loaded via a namespace (and not attached):
 [1] IRanges_2.6.0        parallel_3.3.0       DBI_0.4-1            tools_3.3.0          RCurl_1.95-4.8       Biobase_2.32.0       AnnotationDbi_1.34.3
 [8] RSQLite_1.0.0        S4Vectors_0.10.1     BiocGenerics_0.18.0  stats4_3.3.0         bitops_1.0-6         XML_3.98-1.4        

biomart • 1.4k views
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The error also happens to me.

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Mike Smith ★ 6.5k
@mike-smith
Last seen 3 hours ago
EMBL Heidelberg

This code is working for me at the moment. Are you behind a proxy at all? Maybe you need to set the parameters for that using something like this, where you fill in the appropriate values for your network:

options(RCurlOptions = list(proxy="http://proxy.domain.com:800", proxyuserpwd="myuser:mypassword"))

You can also try the following command, which will use an alternative mirror for ensembl, and print the address it is trying to access so you can check it's working in a browser:

listMarts(host = "asia.ensembl.org", verbose = TRUE)

 

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The function doesn't return an error if the Asian server is queried, but does if the default server is.

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Interesting, given it works for me.  Can you access the page in a browser?  The link to the main site is here:

http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt

The result should be XML, with the root node as <MartRegistry>

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There appears to be a problem with our Asian mirror which we're looking at right now. In the meantime, the main site and other mirrors (uswest and useast) appear to be working fine.
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