Question: Error in the vignette for biomaRt (when accessing an ensembl archive)
0
gravatar for Russ Hyde
13 days ago by
Russ Hyde0
Russ Hyde0 wrote:

In the "Using archived versions ..." section of the vignette for biomaRt (https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.html#using-archived-versions-of-ensembl ) there is an error in the code used to access Ensembl54

## -- Copied from the vignette on 2019-11-06 -- 

listMarts(host = 'may2009.archive.ensembl.org')
##                biomart              version
## 1 ENSEMBL_MART_ENSEMBL           Ensembl 54
## 2     ENSEMBL_MART_SNP Ensembl Variation 54
## 3    ENSEMBL_MART_VEGA              Vega 35
## 4             REACTOME   Reactome(CSHL US) 
## 5     wormbase_current   WormBase (CSHL US)
## 6                pride       PRIDE (EBI UK)
ensembl54 <- useMart(host='may2009.archive.ensembl.org', 
                     biomart='ENSEMBL_MART_ENSEMBL', 
                     dataset='hsapiens_gene_ensembl')
## Error in bmRequest(request = request, verbose = verbose): Internal Server Error (HTTP 500).

Could the vignette be rebuilt and checked to ensure that a working example is used in this section.

I'm separately having issues accessing the may2009 archive - I can only intermittently get results from listMarts(host = "may2009.archive.ensembl.org") so I think the servers may be down at the moment.

All the best

biomart vignette • 47 views
ADD COMMENTlink modified 13 days ago by Mike Smith4.0k • written 13 days ago by Russ Hyde0
Answer: Error in the vignette for biomaRt (when accessing an ensembl archive)
1
gravatar for Mike Smith
13 days ago by
Mike Smith4.0k
EMBL Heidelberg / de.NBI
Mike Smith4.0k wrote:

Thanks for reporting this. At the moment I get the same 'Error 500' if I visit http://may2009.archive.ensembl.org/index.html in a browser, so as you suggest there's probably something wrong with the server.

The list of available mirrors is taken directly from Ensembl so I don't think that archive has been retired. Since the code in itself is correct and any change will take a while to propagate through Bioconductor's build system, I'll leave it as it is in the hope that the archive is only down temporarily. However if this continues to be an issue in a week or so I'll update the example to use a different archive.

ADD COMMENTlink written 13 days ago by Mike Smith4.0k

Thanks for having a look at it Mike

ADD REPLYlink written 13 days ago by Russ Hyde0
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