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
Thanks for having a look at it Mike
Hello there, do you know if this issue have been solved? I have been having the same problems with different archives.
Best,
That partcular issue was just temporary downtime for the achive server and it worked shortly afterwards.
Ensembl are currently moving to a new data centre and some of the archives are not currently available, so you may well get the same error:
You can find some more details at http://www.ensembl.info/2020/02/18/reduced-functionality-16th-25th-march-2020/
Hi! I am having this issue again. Is there a work around other than waiting?