Question: biomaRt changed host issues
0
gravatar for kylvalda
3.6 years ago by
kylvalda0
United States
kylvalda0 wrote:

Biomart has recently changed its server from www.biomart.org to www.ensembl.org

This leads to the following when loading the package:

> library(biomaRt)
> listEnsembl()
[1] biomart version
<0 rows> (or 0-length row.names)
>


a month ago everything was fine:

> listEnsembl()
     biomart               version
1    ensembl      Ensembl Genes 84
2        snp  Ensembl Variation 84
3 regulation Ensembl Regulation 84
4       vega               Vega 64

 

I'm using biomaRt with easyRNASeq to annotate my RNA-Seq data.

 

A suggested workaround is:

listMarts(host = "www.ensembl.org")

 

but that doesn't work for me:

> listMarts(host='www.ensembl.org')
[1] biomart version
<0 rows> (or 0-length row.names)
 

What shall I do? This is quite frustrating. Session Info below. Do I need to upgrade to R 3.3 and biomart 2.28???

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] biomaRt_2.26.1       BiocInstaller_1.20.3

loaded via a namespace (and not attached):
 [1] IRanges_2.4.8        parallel_3.2.1       DBI_0.4-1
 [4] tools_3.2.1          RCurl_1.95-4.8       Biobase_2.30.0
 [7] AnnotationDbi_1.32.3 RSQLite_1.0.0        S4Vectors_0.8.11
[10] BiocGenerics_0.16.1  stats4_3.2.1         bitops_1.0-6
[13] XML_3.98-1.4
 

biomart • 718 views
ADD COMMENTlink modified 3.6 years ago by James W. MacDonald52k • written 3.6 years ago by kylvalda0
Answer: biomaRt changed host issues
0
gravatar for James W. MacDonald
3.6 years ago by
United States
James W. MacDonald52k wrote:

YES! You always need to upgrade to the newest versions. If there are changes to the Biomart at Ensembl, you cannot expect old versions of biomaRt to be upgraded to address that. The only version that is expected to work flawlessly (and the only version that is supported) is the current version.

ADD COMMENTlink written 3.6 years ago by James W. MacDonald52k
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