Error in the vignette for biomaRt (when accessing an ensembl archive)
1
1
Entering edit mode
Russ Hyde ▴ 10
@russ-hyde-22292
Last seen 2.9 years ago

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 • 1.9k views
2
Entering edit mode
Mike Smith ★ 5.7k
@mike-smith
Last seen 2 days ago
EMBL Heidelberg / de.NBI

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.

0
Entering edit mode

Thanks for having a look at it Mike

0
Entering edit mode

Hello there, do you know if this issue have been solved? I have been having the same problems with different archives.

Best,

1
Entering edit mode

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:

Archives Some of our archive sites will be completely unavailable. You will not be able to access any archive websites for non-vertebrates. For vertebrates, archives e88-e98 inclusive will be inaccessible.

You can find some more details at http://www.ensembl.info/2020/02/18/reduced-functionality-16th-25th-march-2020/

0
Entering edit mode

Hi! I am having this issue again. Is there a work around other than waiting?