biomart archive version
2
0
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@raakesh_7111-24370
Last seen 11 months ago

I am trying to use Ensembl archive version via BiomaRT, below is my code

ensembl = useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", 
                  host = "oct2014.archive.ensembl.org")

But I get following error for past one day Error: Failed to load external entity "http://www.ensembl.org/info/website/archives/index.html?redirect=no"

Few weeks before I had the same error, help please.

annotation biomart • 416 views
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@laurent-gatto-5645
Last seen 1 day ago
Belgium

There have been some connection issues with Biomart. I am able to run your code chunk successfully using the development version

> library(biomaRt)
> ensembl = useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", 
                  host = "oct2014.archive.ensembl.org")
> ensembl
Object of class 'Mart':
  Using the ENSEMBL_MART_ENSEMBL BioMart database
  Using the hsapiens_gene_ensembl dataset
> packageVersion("biomaRt")
[1] ‘2.45.5’

but not with the current stable version

> ensembl = useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host = "oct2014.archive.ensembl.org")
Error: failed to load external entity "http://www.ensembl.org/info/website/archives/index.html?redirect=no"
> packageVersion("biomaRt")
[1] '2.44.1'

Mike Smith, the maintainer of biomaRt has posted some instructions here.

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The most recent release version is now 2.44.4 where this problem has hopefully been fixed.

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@raakesh_7111-24370
Last seen 11 months ago

@ Laurent and Mike, many thanks for your help. I fixed the issues by installing version 2.44.4

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