biomaRt package problem
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@stevenvanlaere-9244
Last seen 5.9 years ago
Belgium

All,

anyone recently encountered problems with the biomaRt package?

Steven

 

 

biomart • 2.0k views
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Johannes Rainer ★ 1.9k
@johannes-rainer-6987
Last seen 4 months ago
Italy

without knowing what problem you have it's hard to answer... but eventually you might find a solution to your problem on that post:

biomaRt no longer works with proxy after upgrade

cheers, jo

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Thomas Maurel ▴ 790
@thomas-maurel-5295
Last seen 3 months ago
United Kingdom

Dear Steven,

I am afraid this is because listMarts is looking at the biomart.org website by default which is temporarily down at the moment.

The function accepts an host argument so if you are interested in the Ensembl marts, you can run the following:

> listMarts(host="www.ensembl.org")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 82
2     ENSEMBL_MART_SNP  Ensembl Variation 82
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 82
4    ENSEMBL_MART_VEGA               Vega 62
5                pride        PRIDE (EBI UK)

or 

> listEnsembl()
     biomart               version
1    ensembl      Ensembl Genes 82
2        snp  Ensembl Variation 82
3 regulation Ensembl Regulation 82
4       vega               Vega 62
5      pride        PRIDE (EBI UK)

Then you can connect to the Ensembl marts by running:

ensembl <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", path="/biomart/martservice", dataset="hsapiens_gene_ensembl")

or 

ensembl <- useEnsembl(biomart="ensembl",dataset="hsapiens_gene_ensembl")

You can find more information on the following blog post: http://www.ensembl.info/blog/2015/06/01/biomart-or-how-to-access-the-ensembl-data-from-r/

Hope this helps,

Thomas

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@stevenvanlaere-9244
Last seen 5.9 years ago
Belgium

The problem is that the error messages I get are different depending on time point AND computer.... This is what I get now:

> library(biomaRt)

>listMarts()

Space required after the Public Identifier

SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Opening and ending tag mismatch: hr line 7 and body
Opening and ending tag mismatch: body line 4 and html
Premature end of data in tag html line 2
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 7 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2

> sessionInfo()

R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.1 (El Capitan)

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

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

other attached packages:
[1] biomaRt_2.26.0

loaded via a namespace (and not attached):
 [1] IRanges_2.4.1        parallel_3.2.2       DBI_0.3.1            tools_3.2.2         
 [5] RCurl_1.95-4.7       Biobase_2.30.0       AnnotationDbi_1.32.0 RSQLite_1.0.0       
 [9] S4Vectors_0.8.1      BiocGenerics_0.16.1  stats4_3.2.2         bitops_1.0-6        
[13] XML_3.98-1.3  

Last week I got a message that the BioMart web service was temporarily down...

 

 

 

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Any news on this yet? I'm getting the same problem :/

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Dear Mark,

Please see my answer above: A: biomaRt package problem

Hope this helps,

Regards,

Thomas

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biomaRt has been updated to 2.26.1 in release and 2.27.1 in devel (except for Mac OS 'snow leopard'), to point to ensembl by default. So after updating (via biocLite("biomaRt")) the function listMarts() will work; there may be additional problems with existing scripts or other packages that assume that the connection still points to biomart.org.

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Ooops. Sorry didn't see that. Thanks

Mark

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Thanks!

 

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Thanks!

 

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