I'm having trouble connecting to the human dataset from ensembl. I've run these scripts hundreds of times and this was the first time I've encountered these errors. Anyone can help?
> ensembl <- useMart("ensembl", dataset="hsapiens_gene_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&redirect=no
> ensembl <- useMart("ensembl", host="uswest.ensembl.org", dataset="hsapiens_gene_ensembl", ensemblRedirect = FALSE)
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.
> ensembl <- useMart("ensembl", host="useast.ensembl.org", dataset="hsapiens_gene_ensembl", ensemblRedirect = FALSE)
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.
> ensembl <- useMart("ensembl", host="uswest.ensembl.org", dataset="hsapiens_gene_ensembl", ensemblRedirect = FALSE)
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.
> ensembl = useMart("ensembl", host="uswest.ensembl.org")
> listDatasets(ensembl)
[1] dataset description version
<0 rows> (or 0-length row.names)
> ensembl = useMart("ensembl", host="useast.ensembl.org")
> listDatasets(ensembl)
[1] dataset description version
<0 rows> (or 0-length row.names)
> ensembl = useMart("ensembl", host="asia.ensembl.org")
> listDatasets(ensembl)
[1] dataset description version
<0 rows> (or 0-length row.names)
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.3
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] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.32.1 BiocInstaller_1.26.1 ggcyto_1.4.1
[4] ggplot2_2.2.1 flowWorkspace_3.24.4 ncdfFlow_2.22.2
[7] BH_1.66.0-1 RcppArmadillo_0.8.400.0.0 flowViz_1.40.0
[10] lattice_0.20-35 flowCore_1.42.3 BRRR_1.2
[13] devtools_1.13.5 stringr_1.3.0 VariantAnnotation_1.22.3
[16] Rsamtools_1.28.0 SummarizedExperiment_1.6.5 DelayedArray_0.2.7
[19] matrixStats_0.53.1 RMySQL_0.10.14 DBI_0.8
[22] openxlsx_4.0.17 seqinr_3.4-5 org.Hs.eg.db_3.4.1
[25] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.28.5 AnnotationDbi_1.38.2
[28] Biobase_2.36.2 BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.44.2
[31] rtracklayer_1.36.6 GenomicRanges_1.28.6 GenomeInfoDb_1.12.3
[34] CRISPRseek_1.16.0 Biostrings_2.44.2 XVector_0.16.0
[37] IRanges_2.10.5 S4Vectors_0.14.7 BiocGenerics_0.22.1
loaded via a namespace (and not attached):
[1] bitops_1.0-6 bit64_0.9-7 progress_1.1.2 httr_1.3.1
[5] RColorBrewer_1.1-2 Rgraphviz_2.20.0 tools_3.4.1 R6_2.2.2
[9] KernSmooth_2.23-15 lazyeval_0.2.1 colorspace_1.3-2 ade4_1.7-11
[13] withr_2.1.2 prettyunits_1.0.2 gridExtra_2.3 curl_3.2
[17] git2r_0.21.0 bit_1.1-12 compiler_3.4.1 graph_1.54.0
[21] scales_0.5.0 DEoptimR_1.0-8 hexbin_1.27.2 mvtnorm_1.0-7
[25] robustbase_0.93-0 digest_0.6.15 rrcov_1.4-3 pkgconfig_2.0.1
[29] rlang_0.2.0 RSQLite_2.1.0 bindr_0.1.1 BiocParallel_1.10.1
[33] dplyr_0.7.4 RCurl_1.95-4.10 magrittr_1.5 GenomeInfoDbData_0.99.0
[37] Matrix_1.2-14 Rcpp_0.12.16 munsell_0.4.3 stringi_1.1.7
[41] yaml_2.1.18 MASS_7.3-49 zlibbioc_1.22.0 plyr_1.8.4
[45] grid_3.4.1 blob_1.1.1 hash_2.2.6 knitr_1.20
[49] pillar_1.2.2 corpcor_1.6.9 XML_3.98-1.11 glue_1.2.0
[53] latticeExtra_0.6-28 data.table_1.10.4-3 gtable_0.2.0 assertthat_0.2.0
[57] IDPmisc_1.1.17 pcaPP_1.9-73 audio_0.1-5 tibble_1.4.2
[61] GenomicAlignments_1.12.2 memoise_1.1.0 bindrcpp_0.2.2 cluster_2.0.7-1
Thanks, I get the same with ensemblRedirect = FALSE
The "down" status is probably what I've encountered.
Interesting, for me this works on machine both in Europe and the US:
Maybe a local issue (middle east). The bit bucket doesn't pour my way...
> ensembl = useMart("ensembl", host="useast.ensembl.org", ensemblRedirect = FALSE)
> ensembl
Object of class 'Mart':
Using the ENSEMBL_MART_ENSEMBL BioMart database
Using the dataset
> dim(listDatasets(ensembl))
[1] 0 3