Question

Unexpected format to the list of available marts error (12/11/2017)

1

Entering edit mode

jennifer.cw.hu ▴ 10

@jennifercwhu-14601

Last seen 6.4 years ago

Hi,

I have run into an issue with the listMarts function. When I type in useMart, the following error comes up:

ensembl<-useMart("ensembl")
Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE, :
Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt

The sessionInfo is as follows:

R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] biomaRt_2.32.1 BiocInstaller_1.26.1 DESeq_1.28.0 lattice_0.20-35 locfit_1.5-9.1
[6] Biobase_2.36.2 BiocGenerics_0.22.1

loaded via a namespace (and not attached):
[1] Rcpp_0.12.14 AnnotationDbi_1.38.2 splines_3.4.1 IRanges_2.10.5
[5] bit_1.1-12 xtable_1.8-2 rlang_0.1.4 blob_1.1.0
[9] tools_3.4.1 grid_3.4.1 DBI_0.7 genefilter_1.58.1
[13] survival_2.41-3 digest_0.6.12 bit64_0.9-7 tibble_1.3.4
[17] Matrix_1.2-12 RColorBrewer_1.1-2 geneplotter_1.54.0 S4Vectors_0.14.7
[21] bitops_1.0-6 RCurl_1.95-4.8 memoise_1.1.0 RSQLite_2.0
[25] compiler_3.4.1 stats4_3.4.1 XML_3.98-1.9 annotate_1.54.0

I checked the URL and ?listMarts which said to report the issue. When I check the above URL, it does start with <MartRegistry>. I was able to run this fine on Friday evening (Dec 8, 2017) and am wondering why it no longer works. I am very new to Bioconductor and any help would be appreciated.

Thanks!
Jen

problem with biomart's listmarts function • 2.1k views

ADD COMMENT • link updated 6.4 years ago by James W. MacDonald 65k • written 6.4 years ago by jennifer.cw.hu ▴ 10

0

Entering edit mode

I can confirm the present server issues.

Below, for example, the first two requests below succeed and the later two fail:

> useMart(biomart='ensembl', dataset='hsapiens_gene_ensembl', host='www.ensembl.org')
Object of class 'Mart':
  Using the ENSEMBL_MART_ENSEMBL BioMart database
  Using the hsapiens_gene_ensembl dataset> 
> useMart(biomart='ensembl', dataset='hsapiens_gene_ensembl', host='www.ensembl.org')
Object of class 'Mart':
  Using the ENSEMBL_MART_ENSEMBL BioMart database
  Using the hsapiens_gene_ensembl dataset> 
> useMart(biomart='ensembl', dataset='hsapiens_gene_ensembl', host='www.ensembl.org')
Error in checkDataset(dataset = dataset, mart = mart) : 
  The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.
Calls: useMart -> useDataset -> checkDataset
> useMart(biomart='ensembl', dataset='hsapiens_gene_ensembl', host='www.ensembl.org', verbose=TRUE)
Attempting web service request:
http://www.ensembl.org:80/biomart/martservice?type=version&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL
   V1
1 0.7
BioMartServer running BioMart version: 0.7
Mart virtual schema: default
Mart host: http://www.ensembl.org:80/biomart/martservice
Error in checkDataset(dataset = dataset, mart = mart) : 
  The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.
Calls: useMart -> useDataset -> checkDataset

The same issue when using archive.ensembl.org. Has been happening since this morning or so.

Usually when this happens, switching to one of the archive servers or waiting a day or so resolves the issue. It would be nice if there was a way to print the server response associated with the failed request to see exactly what is going on.

Best,

Keith

ADD REPLY • link 6.4 years ago Keith Hughitt ▴ 180

score 0 · Answer 1 · 2017-12-11

0

Entering edit mode

James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 18 hours ago

United States

Sometimes web resources go on the fritz momentarily. When I try to use biomaRt, it works fine:

> ensembl <- useMart("ensembl")
> listMarts(ensembl)
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 91
2   ENSEMBL_MART_MOUSE      Mouse strains 91
3     ENSEMBL_MART_SNP  Ensembl Variation 91
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 91

So maybe it's just a matter of trying again.

ADD COMMENT • link 6.4 years ago James W. MacDonald 65k

0

Entering edit mode

I tried again and the same error is still coming up :(

ADD REPLY • link 6.4 years ago jennifer.cw.hu ▴ 10